0.1_prepare_kallisto_quant

Context

For EnPACT training, it is best to use transcript counts to compute expression. This is because the transcript counts are more accurate than gene counts if transcript length normalization is required.

Convert bam files to fastq files

Kallisto requires fastq files as input, and I have RNAseq files currently. Therefore I will convert the bam files to fastq files using the bedtools bamtofastq command.

Code

# import glob
# import os
# import subprocess

# path_to_bedtools = "/beagle3/haky/users/saideep/software/bedtools2/bin"

# path_to_bams = "/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq"

# bam_files = glob.glob(path_to_bams + "/*.bam")

# for bam_file in bam_files:
#     print(bam_file)
    
#     cmd = [
#         "sbatch",
#         "/beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch",
#         bam_file,
#         bam_file.replace(".bam", ".fastq")
#     ]
#     print(" ".join(cmd))
#     os.system(" ".join(cmd))
#     print("Done")

/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF02_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF02_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF02_NI.sorted.mdup.fastq
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU47_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU47_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU47_Flu.sorted.mdup.fastq
Submitted batch job 18133318
Submitted batch job 18133320
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU19_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU19_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU19_NI.sorted.mdup.fastq
Submitted batch job 18133321
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU39_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU39_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU39_NI.sorted.mdup.fastq
Submitted batch job 18133322
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU41_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU41_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU41_Flu.sorted.mdup.fastq
Submitted batch job 18133323
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF28_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF28_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF28_Flu.sorted.mdup.fastq
Submitted batch job 18133324
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF04_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF04_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF04_Flu.sorted.mdup.fastq
Submitted batch job 18133325
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU05_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU05_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU05_Flu.sorted.mdup.fastq
Submitted batch job 18133326
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF22_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF22_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF22_NI.sorted.mdup.fastq
Submitted batch job 18133327
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU29_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU29_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU29_Flu.sorted.mdup.fastq
Submitted batch job 18133328
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU15_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU15_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU15_Flu.sorted.mdup.fastq
Submitted batch job 18133329
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF26_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF26_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF26_NI.sorted.mdup.fastq
Submitted batch job 18133330
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU41_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU41_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU41_NI.sorted.mdup.fastq
Submitted batch job 18133331
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU19_Mock.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU19_Mock.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU19_Mock.sorted.mdup.fastq
Submitted batch job 18133332
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU21_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU21_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU21_Flu.sorted.mdup.fastq
Submitted batch job 18133334
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF32_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF32_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF32_Flu.sorted.mdup.fastq
Submitted batch job 18133335
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU31_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU31_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU31_Flu.sorted.mdup.fastq
Submitted batch job 18133336
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU27_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU27_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU27_Flu.sorted.mdup.fastq
Submitted batch job 18133337
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU21_Mock.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU21_Mock.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU21_Mock.sorted.mdup.fastq
Submitted batch job 18133338
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF30_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF30_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF30_NI.sorted.mdup.fastq
Submitted batch job 18133339
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF12_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF12_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF12_NI.sorted.mdup.fastq
Submitted batch job 18133340
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU03_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU03_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU03_NI.sorted.mdup.fastq
Submitted batch job 18133341
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF32_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF32_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF32_NI.sorted.mdup.fastq
Submitted batch job 18133342
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF22_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF22_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF22_Flu.sorted.mdup.fastq
Submitted batch job 18133343
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU43_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU43_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU43_NI.sorted.mdup.fastq
Submitted batch job 18133344
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF06_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF06_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF06_NI.sorted.mdup.fastq
Submitted batch job 18133345
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF28_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF28_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF28_NI.sorted.mdup.fastq
Submitted batch job 18133346
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU122_iPSCS_D81_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU122_iPSCS_D81_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU122_iPSCS_D81_NI.sorted.mdup.fastq
Submitted batch job 18133347
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF18_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF18_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF18_Flu.sorted.mdup.fastq
Submitted batch job 18133349
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU13_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU13_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU13_NI.sorted.mdup.fastq
Submitted batch job 18133350
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU122_iPSCs_D53_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU122_iPSCs_D53_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU122_iPSCs_D53_NI.sorted.mdup.fastq
Submitted batch job 18133351
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU09_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU09_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU09_Flu.sorted.mdup.fastq
Submitted batch job 18133352
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF38_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF38_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF38_Flu.sorted.mdup.fastq
Submitted batch job 18133353
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF02_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF02_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF02_Flu.sorted.mdup.fastq
Submitted batch job 18133354
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF04_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF04_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF04_NI.sorted.mdup.fastq
Submitted batch job 18133355
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF24_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF24_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF24_NI.sorted.mdup.fastq
Submitted batch job 18133356
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU17_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU17_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU17_Flu.sorted.mdup.fastq
Submitted batch job 18133357
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF38_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF38_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF38_NI.sorted.mdup.fastq
Submitted batch job 18133358
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF14_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF14_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF14_Flu.sorted.mdup.fastq
Submitted batch job 18133359
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF12_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF12_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF12_Flu.sorted.mdup.fastq
Submitted batch job 18133360
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU07_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU07_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU07_Flu.sorted.mdup.fastq
Submitted batch job 18133361
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF36_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF36_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF36_NI.sorted.mdup.fastq
Submitted batch job 18133362
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU33_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU33_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU33_Flu.sorted.mdup.fastq
Submitted batch job 18133364
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU37_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU37_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU37_NI.sorted.mdup.fastq
Submitted batch job 18133365
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF10_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF10_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF10_Flu.sorted.mdup.fastq
Submitted batch job 18133366
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU33_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU33_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU33_NI.sorted.mdup.fastq
Submitted batch job 18133367
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF20_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF20_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF20_Flu.sorted.mdup.fastq
Submitted batch job 18133368
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF16_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF16_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF16_Flu.sorted.mdup.fastq
Submitted batch job 18133369
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU21_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU21_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU21_NI.sorted.mdup.fastq
Submitted batch job 18133370
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF30_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF30_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF30_Flu.sorted.mdup.fastq
Submitted batch job 18133371
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU01_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU01_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU01_Flu.sorted.mdup.fastq
Submitted batch job 18133372
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU01_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU01_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU01_NI.sorted.mdup.fastq
Submitted batch job 18133373
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU27_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU27_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU27_NI.sorted.mdup.fastq
Submitted batch job 18133374
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU43_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU43_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU43_Flu.sorted.mdup.fastq
Submitted batch job 18133375
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF36_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF36_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF36_Flu.sorted.mdup.fastq
Submitted batch job 18133376
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU37_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU37_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU37_Flu.sorted.mdup.fastq
Submitted batch job 18133377
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF08_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF08_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF08_NI.sorted.mdup.fastq
Submitted batch job 18133379
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF08_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF08_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF08_Flu.sorted.mdup.fastq
Submitted batch job 18133380
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU17_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU17_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU17_NI.sorted.mdup.fastq
Submitted batch job 18133381
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU47_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU47_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU47_NI.sorted.mdup.fastq
Submitted batch job 18133382
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF10_Mock.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF10_Mock.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF10_Mock.sorted.mdup.fastq
Submitted batch job 18133383
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF14_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF14_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF14_NI.sorted.mdup.fastq
Submitted batch job 18133384
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU15_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU15_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU15_NI.sorted.mdup.fastq
Submitted batch job 18133385
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF20_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF20_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF20_NI.sorted.mdup.fastq
Submitted batch job 18133386
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF16_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF16_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF16_NI.sorted.mdup.fastq
Submitted batch job 18133387
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU25_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU25_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU25_NI.sorted.mdup.fastq
Submitted batch job 18133388
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF08_Mock.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF08_Mock.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF08_Mock.sorted.mdup.fastq
Submitted batch job 18133389
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF06_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF06_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF06_Flu.sorted.mdup.fastq
Submitted batch job 18133390
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU25_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU25_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU25_Flu.sorted.mdup.fastq
Submitted batch job 18133391
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU09_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU09_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU09_NI.sorted.mdup.fastq
Submitted batch job 18133392
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU39_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU39_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU39_Flu.sorted.mdup.fastq
Submitted batch job 18133394
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU19_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU19_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU19_Flu.sorted.mdup.fastq
Submitted batch job 18133395
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF24_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF24_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF24_Flu.sorted.mdup.fastq
Submitted batch job 18133396
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU31_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU31_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU31_NI.sorted.mdup.fastq
Submitted batch job 18133397
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF26_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF26_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF26_Flu.sorted.mdup.fastq
Submitted batch job 18133398
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF10_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF10_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF10_NI.sorted.mdup.fastq
Submitted batch job 18133399
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF34_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF34_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF34_Flu.sorted.mdup.fastq
Submitted batch job 18133400
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU122_iPSCs_D81_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU122_iPSCs_D81_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU122_iPSCs_D81_Flu.sorted.mdup.fastq
Submitted batch job 18133401
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU29_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU29_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU29_NI.sorted.mdup.fastq
Submitted batch job 18133402
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU03_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU03_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU03_Flu.sorted.mdup.fastq
Submitted batch job 18133403
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU13_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU13_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU13_Flu.sorted.mdup.fastq
Submitted batch job 18133404
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF34_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF34_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF34_NI.sorted.mdup.fastq
Submitted batch job 18133405
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF18_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF18_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF18_NI.sorted.mdup.fastq
Submitted batch job 18133406
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU05_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU05_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU05_NI.sorted.mdup.fastq
Submitted batch job 18133407
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU122_iPSCs_D53_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU122_iPSCs_D53_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU122_iPSCs_D53_Flu.sorted.mdup.fastq
Submitted batch job 18133408
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU07_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU07_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU07_NI.sorted.mdup.fastq
Submitted batch job 18133410
Done

Run Kallisto quant

Prepare kallisto files

Code

path_to_kallisto_bin = "/beagle3/haky/users/saideep/software/kallisto/build/src/kallisto"

path_to_kallisto_index_dir = "/beagle3/haky/users/saideep/software/kallisto/ref"

Code

import glob
import os
import subprocess

path_to_bedtools = "/beagle3/haky/users/saideep/software/bedtools2/bin"

path_to_bams = "/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq"

bam_files = glob.glob(path_to_bams + "/*.bam")

output_dir = "/beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs"

for bam_file in bam_files:
    print(bam_file)
    
    cur_output_dir = os.path.join(output_dir,os.path.basename(bam_file).replace(".bam",""))
    os.makedirs(cur_output_dir, exist_ok=True)

    cmd = [
        "sbatch",
        "/beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch",
        bam_file,
        bam_file.replace(".bam", ".fastq"),
        path_to_kallisto_bin,
        os.path.join(path_to_kallisto_index_dir,"index.idx"),
        cur_output_dir
    ]
    print(" ".join(cmd))
    os.system(" ".join(cmd))
    print("Done")

/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF02_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF02_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF02_NI.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/AF02_NI.sorted.mdup
Submitted batch job 18213969
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU47_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU47_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU47_Flu.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU47_Flu.sorted.mdup
Submitted batch job 18213970
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU19_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU19_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU19_NI.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU19_NI.sorted.mdup
Submitted batch job 18213971
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU39_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU39_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU39_NI.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU39_NI.sorted.mdup
Submitted batch job 18213972
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU41_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU41_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU41_Flu.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU41_Flu.sorted.mdup
Submitted batch job 18213973
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF28_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF28_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF28_Flu.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/AF28_Flu.sorted.mdup
Submitted batch job 18213974
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF04_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF04_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF04_Flu.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/AF04_Flu.sorted.mdup
Submitted batch job 18213975
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU05_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU05_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU05_Flu.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU05_Flu.sorted.mdup
Submitted batch job 18213976
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF22_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF22_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF22_NI.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/AF22_NI.sorted.mdup
Submitted batch job 18213977
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU29_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU29_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU29_Flu.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU29_Flu.sorted.mdup
Submitted batch job 18213978
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU15_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU15_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU15_Flu.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU15_Flu.sorted.mdup
Submitted batch job 18213979
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF26_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF26_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF26_NI.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/AF26_NI.sorted.mdup
Submitted batch job 18213980
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU41_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU41_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU41_NI.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU41_NI.sorted.mdup
Submitted batch job 18213981
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU19_Mock.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU19_Mock.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU19_Mock.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU19_Mock.sorted.mdup
Submitted batch job 18213982
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU21_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU21_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU21_Flu.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU21_Flu.sorted.mdup
Submitted batch job 18213983
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF32_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF32_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF32_Flu.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/AF32_Flu.sorted.mdup
Submitted batch job 18213984
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU31_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU31_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU31_Flu.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU31_Flu.sorted.mdup
Submitted batch job 18213985
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU27_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU27_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU27_Flu.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU27_Flu.sorted.mdup
Submitted batch job 18213986
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU21_Mock.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU21_Mock.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU21_Mock.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU21_Mock.sorted.mdup
Submitted batch job 18213987
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF30_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF30_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF30_NI.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/AF30_NI.sorted.mdup
Submitted batch job 18213988
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF12_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF12_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF12_NI.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/AF12_NI.sorted.mdup
Submitted batch job 18213989
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU03_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU03_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU03_NI.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU03_NI.sorted.mdup
Submitted batch job 18213990
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF32_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF32_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF32_NI.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/AF32_NI.sorted.mdup
Submitted batch job 18213991
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF22_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF22_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF22_Flu.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/AF22_Flu.sorted.mdup
Submitted batch job 18213992
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU43_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU43_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU43_NI.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU43_NI.sorted.mdup
Submitted batch job 18213993
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF06_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF06_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF06_NI.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/AF06_NI.sorted.mdup
Submitted batch job 18213994
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF28_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF28_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF28_NI.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/AF28_NI.sorted.mdup
Submitted batch job 18213995
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU122_iPSCS_D81_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU122_iPSCS_D81_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU122_iPSCS_D81_NI.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU122_iPSCS_D81_NI.sorted.mdup
Submitted batch job 18213996
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF18_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF18_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF18_Flu.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/AF18_Flu.sorted.mdup
Submitted batch job 18213997
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU13_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU13_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU13_NI.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU13_NI.sorted.mdup
Submitted batch job 18213998
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU122_iPSCs_D53_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU122_iPSCs_D53_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU122_iPSCs_D53_NI.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU122_iPSCs_D53_NI.sorted.mdup
Submitted batch job 18213999
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU09_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU09_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU09_Flu.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU09_Flu.sorted.mdup
Submitted batch job 18214000
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF38_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF38_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF38_Flu.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/AF38_Flu.sorted.mdup
Submitted batch job 18214001
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF02_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF02_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF02_Flu.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/AF02_Flu.sorted.mdup
Submitted batch job 18214002
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF04_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF04_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF04_NI.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/AF04_NI.sorted.mdup
Submitted batch job 18214003
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF24_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF24_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF24_NI.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/AF24_NI.sorted.mdup
Submitted batch job 18214004
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU17_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU17_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU17_Flu.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU17_Flu.sorted.mdup
Submitted batch job 18214005
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF38_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF38_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF38_NI.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/AF38_NI.sorted.mdup
Submitted batch job 18214006
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF14_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF14_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF14_Flu.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/AF14_Flu.sorted.mdup
Submitted batch job 18214007
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF12_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF12_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF12_Flu.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/AF12_Flu.sorted.mdup
Submitted batch job 18214008
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU07_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU07_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU07_Flu.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU07_Flu.sorted.mdup
Submitted batch job 18214009
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF36_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF36_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF36_NI.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/AF36_NI.sorted.mdup
Submitted batch job 18214010
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU33_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU33_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU33_Flu.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU33_Flu.sorted.mdup
Submitted batch job 18214011
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU37_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU37_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU37_NI.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU37_NI.sorted.mdup
Submitted batch job 18214012
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF10_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF10_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF10_Flu.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/AF10_Flu.sorted.mdup
Submitted batch job 18214013
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU33_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU33_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU33_NI.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU33_NI.sorted.mdup
Submitted batch job 18214014
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF20_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF20_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF20_Flu.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/AF20_Flu.sorted.mdup
Submitted batch job 18214015
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF16_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF16_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF16_Flu.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/AF16_Flu.sorted.mdup
Submitted batch job 18214016
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU21_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU21_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU21_NI.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU21_NI.sorted.mdup
Submitted batch job 18214017
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF30_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF30_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF30_Flu.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/AF30_Flu.sorted.mdup
Submitted batch job 18214018
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU01_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU01_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU01_Flu.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU01_Flu.sorted.mdup
Submitted batch job 18214019
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU01_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU01_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU01_NI.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU01_NI.sorted.mdup
Submitted batch job 18214020
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU27_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU27_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU27_NI.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU27_NI.sorted.mdup
Submitted batch job 18214021
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU43_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU43_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU43_Flu.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU43_Flu.sorted.mdup
Submitted batch job 18214022
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF36_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF36_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF36_Flu.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/AF36_Flu.sorted.mdup
Submitted batch job 18214023
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU37_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU37_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU37_Flu.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU37_Flu.sorted.mdup
Submitted batch job 18214024
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF08_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF08_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF08_NI.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/AF08_NI.sorted.mdup
Submitted batch job 18214025
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF08_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF08_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF08_Flu.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/AF08_Flu.sorted.mdup
Submitted batch job 18214026
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU17_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU17_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU17_NI.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU17_NI.sorted.mdup
Submitted batch job 18214027
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU47_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU47_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU47_NI.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU47_NI.sorted.mdup
Submitted batch job 18214028
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF10_Mock.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF10_Mock.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF10_Mock.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/AF10_Mock.sorted.mdup
Submitted batch job 18214029
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF14_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF14_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF14_NI.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/AF14_NI.sorted.mdup
Submitted batch job 18214030
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU15_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU15_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU15_NI.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU15_NI.sorted.mdup
Submitted batch job 18214031
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF20_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF20_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF20_NI.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/AF20_NI.sorted.mdup
Submitted batch job 18214032
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF16_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF16_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF16_NI.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/AF16_NI.sorted.mdup
Submitted batch job 18214033
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU25_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU25_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU25_NI.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU25_NI.sorted.mdup
Submitted batch job 18214034
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF08_Mock.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF08_Mock.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF08_Mock.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/AF08_Mock.sorted.mdup
Submitted batch job 18214035
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF06_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF06_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF06_Flu.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/AF06_Flu.sorted.mdup
Submitted batch job 18214036
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU25_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU25_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU25_Flu.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU25_Flu.sorted.mdup
Submitted batch job 18214037
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU09_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU09_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU09_NI.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU09_NI.sorted.mdup
Submitted batch job 18214038
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU39_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU39_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU39_Flu.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU39_Flu.sorted.mdup
Submitted batch job 18214039
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU19_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU19_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU19_Flu.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU19_Flu.sorted.mdup
Submitted batch job 18214040
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF24_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF24_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF24_Flu.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/AF24_Flu.sorted.mdup
Submitted batch job 18214041
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU31_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU31_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU31_NI.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU31_NI.sorted.mdup
Submitted batch job 18214042
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF26_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF26_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF26_Flu.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/AF26_Flu.sorted.mdup
Submitted batch job 18214043
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF10_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF10_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF10_NI.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/AF10_NI.sorted.mdup
Submitted batch job 18214044
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF34_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF34_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF34_Flu.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/AF34_Flu.sorted.mdup
Submitted batch job 18214045
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU122_iPSCs_D81_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU122_iPSCs_D81_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU122_iPSCs_D81_Flu.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU122_iPSCs_D81_Flu.sorted.mdup
Submitted batch job 18214046
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU29_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU29_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU29_NI.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU29_NI.sorted.mdup
Submitted batch job 18214047
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU03_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU03_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU03_Flu.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU03_Flu.sorted.mdup
Submitted batch job 18214048
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU13_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU13_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU13_Flu.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU13_Flu.sorted.mdup
Submitted batch job 18214049
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF34_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF34_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF34_NI.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/AF34_NI.sorted.mdup
Submitted batch job 18214050
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF18_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF18_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF18_NI.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/AF18_NI.sorted.mdup
Submitted batch job 18214051
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU05_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU05_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU05_NI.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU05_NI.sorted.mdup
Submitted batch job 18214052
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU122_iPSCs_D53_Flu.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU122_iPSCs_D53_Flu.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU122_iPSCs_D53_Flu.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU122_iPSCs_D53_Flu.sorted.mdup
Submitted batch job 18214053
Done
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU07_NI.sorted.mdup.bam
sbatch /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/run_bedtools_to_fastq_kallisto.sbatch /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU07_NI.sorted.mdup.bam /beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU07_NI.sorted.mdup.fastq /beagle3/haky/users/saideep/software/kallisto/build/src/kallisto /beagle3/haky/users/saideep/software/kallisto/ref/index.idx /beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs/EU07_NI.sorted.mdup
Submitted batch job 18214054
Done

Collect output

Code

import pandas as pd
import os,sys
import glob

path_to_bedtools = "/beagle3/haky/users/saideep/software/bedtools2/bin"

path_to_bams = "/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq"

bam_files = glob.glob(path_to_bams + "/*.bam")

output_dir = "/beagle3/haky/users/saideep/github_repos/Daily-Blog-Sai/posts/2023-11-27-normalize_expression_GTEx/kallisto_outputs"

norm_abundance_dict = {}

for bam_file in bam_files:
    print(bam_file)
    
    cur_sample = os.path.basename(bam_file).replace(".bam","").split(".")[0]
    cur_output_dir = os.path.join(output_dir,os.path.basename(bam_file).replace(".bam",""))

    cur_abundance_df = pd.read_csv(os.path.join(cur_output_dir,"abundance.tsv"),sep="\t")
    cur_abundance_df["lnorm_counts"] = cur_abundance_df["est_counts"]/cur_abundance_df["eff_length"]

    norm_abundance_dict[cur_sample] = cur_abundance_df["lnorm_counts"]

    transcripts = cur_abundance_df["target_id"]

transcript_df = pd.DataFrame(norm_abundance_dict)
    

/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF02_NI.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU47_Flu.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU19_NI.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU39_NI.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU41_Flu.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF28_Flu.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF04_Flu.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU05_Flu.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF22_NI.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU29_Flu.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU15_Flu.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF26_NI.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU41_NI.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU19_Mock.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU21_Flu.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF32_Flu.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU31_Flu.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU27_Flu.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU21_Mock.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF30_NI.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF12_NI.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU03_NI.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF32_NI.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF22_Flu.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU43_NI.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF06_NI.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF28_NI.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU122_iPSCS_D81_NI.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF18_Flu.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU13_NI.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU122_iPSCs_D53_NI.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU09_Flu.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF38_Flu.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF02_Flu.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF04_NI.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF24_NI.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU17_Flu.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF38_NI.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF14_Flu.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF12_Flu.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU07_Flu.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF36_NI.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU33_Flu.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU37_NI.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF10_Flu.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU33_NI.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF20_Flu.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF16_Flu.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU21_NI.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF30_Flu.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU01_Flu.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU01_NI.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU27_NI.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU43_Flu.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF36_Flu.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU37_Flu.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF08_NI.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF08_Flu.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU17_NI.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU47_NI.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF10_Mock.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF14_NI.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU15_NI.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF20_NI.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF16_NI.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU25_NI.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF08_Mock.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF06_Flu.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU25_Flu.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU09_NI.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU39_Flu.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU19_Flu.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF24_Flu.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU31_NI.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF26_Flu.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF10_NI.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF34_Flu.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU122_iPSCs_D81_Flu.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU29_NI.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU03_Flu.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU13_Flu.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF34_NI.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/AF18_NI.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU05_NI.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU122_iPSCs_D53_Flu.sorted.mdup.bam
/beagle3/haky/users/saideep/projects/aracena_modeling/bams/RNAseq/EU07_NI.sorted.mdup.bam

Code

transcript_df.index = transcripts
transcript_df_no_ipsc = transcript_df.drop(columns=[x for x in transcript_df.columns if "iPSC" in x])
transcript_df_no_ipsc

	AF02_NI	EU47_Flu	EU19_NI	EU39_NI	EU41_Flu	AF28_Flu	AF04_Flu	EU05_Flu	AF22_NI	EU29_Flu	...	AF26_Flu	AF10_NI	AF34_Flu	EU29_NI	EU03_Flu	EU13_Flu	AF34_NI	AF18_NI	EU05_NI	EU07_NI
target_id
ENST00000308647.8	0.084914	0.229218	0.170867	0.090306	0.162616	0.026455	0.048672	0.089532	0.168973	0.080600	...	0.098139	0.140310	0.136735	0.113186	0.054524	0.060416	0.102310	0.055274	0.137031	0.159632
ENST00000378736.3	0.306737	0.382298	0.393470	0.297024	0.327759	0.034529	0.080107	0.198621	0.399508	0.096716	...	0.147897	0.294790	0.232437	0.231622	0.270864	0.213246	0.402660	0.207183	0.263876	0.435648
ENST00000472194.6	0.113899	0.086293	0.167174	0.060668	0.109784	0.025126	0.016804	0.058208	0.132529	0.047600	...	0.040149	0.117691	0.078191	0.118218	0.052735	0.053334	0.151368	0.141052	0.122641	0.148566
ENST00000474481.1	0.080630	0.055047	0.102692	0.040722	0.029849	0.011634	0.011918	0.033916	0.096149	0.026582	...	0.029797	0.077349	0.054924	0.116864	0.025389	0.020380	0.109426	0.069360	0.106314	0.125809
ENST00000485748.5	0.074259	0.074202	0.070261	0.036636	0.052556	0.009580	0.011541	0.033470	0.111144	0.035407	...	0.019484	0.095357	0.043236	0.059613	0.036442	0.030607	0.081735	0.071918	0.077369	0.101255
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
ENST00000619729.1	0.000000	0.000000	0.000000	0.007162	0.000000	0.000000	0.000000	0.000000	0.000000	0.000000	...	0.000000	0.016329	0.000000	0.000000	0.000000	0.000000	0.000000	0.000000	0.000000	0.000000
ENST00000612640.4	2.012598	0.252251	1.839053	4.708294	0.213299	0.254988	0.110279	0.177215	2.543902	0.128485	...	0.412270	5.447298	0.495141	1.922811	0.367336	0.158622	3.319375	5.896480	1.131111	1.450813
ENST00000614336.4	3.869165	0.559322	3.059576	5.443070	0.685073	0.290628	0.190162	0.234820	2.848416	0.359876	...	0.728716	9.453761	0.700289	4.048664	0.372370	0.436655	9.094296	7.541995	2.400083	2.425489
ENST00000601199.2	0.000000	0.000000	0.000000	0.004866	0.058394	0.000000	0.004866	0.000000	0.000000	0.000000	...	0.000000	0.019465	0.000000	0.000000	0.000000	0.000000	0.000000	0.000000	0.000000	0.009794
ENST00000612315.1	0.050503	0.000000	0.001366	0.001366	0.004098	0.000000	0.002732	0.003737	0.000000	0.001366	...	0.000000	0.000000	0.001366	0.000000	0.001366	0.000000	0.000000	0.000000	0.001366	0.004098

227665 rows × 82 columns

Code

transcript_to_gene_path = "/beagle3/haky/users/saideep/software/kallisto/ref/t2g.txt"

t2g = pd.read_csv(transcript_to_gene_path,sep="\t",header=None)
t2g_columns = ["transcript","gene_id","gene_name"]
for i in range(3,len(t2g.columns)):
    t2g_columns.append("extra_"+str(i))
t2g.columns = t2g_columns
t2g_mapping = {}

for i in range(t2g.shape[0]):
    t2g_mapping[t2g.iloc[i,0]] = t2g.iloc[i,1]

Code

transcript_df_no_ipsc["genes"] = [t2g_mapping[x] for x in transcript_df_no_ipsc.index]

Code

summed_gene_df = transcript_df_no_ipsc.groupby("genes").sum()
summed_gene_df.index.name = None
summed_gene_df.index = [x.split(".")[0] for x in summed_gene_df.index]
summed_gene_df.head()

	AF02_NI	EU47_Flu	EU19_NI	EU39_NI	EU41_Flu	AF28_Flu	AF04_Flu	EU05_Flu	AF22_NI	EU29_Flu	...	AF26_Flu	AF10_NI	AF34_Flu	EU29_NI	EU03_Flu	EU13_Flu	AF34_NI	AF18_NI	EU05_NI	EU07_NI
ENSG00000000003	0.000000	0.003685	0.002726	0.001908	0.008322	0.003745	0.001248	0.001363	0.011732	0.000000	...	0.001635	0.006242	0.003297	0.000545	0.002774	0.004994	0.003543	0.002453	0.000273	0.002774
ENSG00000000005	0.000000	0.001808	0.000000	0.000000	0.007233	0.000000	0.001808	0.000000	0.000000	0.000000	...	0.000000	0.004515	0.001808	0.000000	0.000000	0.000000	0.000000	0.000000	0.000000	0.000000
ENSG00000000419	2.960758	2.810369	1.734147	2.399844	3.093390	0.993989	1.061945	2.441925	2.345439	1.215807	...	2.113905	4.197667	3.480657	1.860930	2.105139	2.276287	4.751472	3.601922	2.444415	2.232910
ENSG00000000457	0.801127	1.239950	0.755215	1.142966	1.044356	0.416660	0.416950	1.115472	0.757761	0.481060	...	1.163611	1.917600	1.387291	0.907438	0.826494	0.807344	1.894002	1.443867	1.068486	1.011204
ENSG00000000460	1.230819	0.243243	0.766251	1.165884	0.215695	0.123144	0.086594	0.207699	0.855321	0.080411	...	0.245065	1.773991	0.235863	0.977696	0.217821	0.116877	2.048346	1.553866	1.262677	1.600131

5 rows × 82 columns

Code

summed_gene_df.to_csv("/beagle3/haky/users/saideep/projects/aracena_modeling/Inputs/counts_matrices/kallisto_counts.tsv",sep="\t", index_label=None)