diagnose_training_tracks_issue

Author

Saideep Gona

Published

September 20, 2023

Code

suppressMessages(library(tidyverse))
suppressMessages(library(glue))
PRE = "/Users/saideepgona/Library/CloudStorage/Box-Box/imlab-data/data-Github/Daily-Blog-Sai"

## COPY THE DATE AND SLUG fields FROM THE HEADER
SLUG="diagnose_training_tracks_issue" ## copy the slug from the header
bDATE='2023-09-20' ## copy the date from the blog's header here
DATA = glue("{PRE}/{bDATE}-{SLUG}")
if(!file.exists(DATA)) system(glue::glue("mkdir {DATA}"))
WORK=DATA

---
title: "diagnose_training_tracks_issue"
author: "Saideep Gona"
date: "2023-09-20"
format:
  html:
    code-fold: true
    code-summary: "Show the code"
execute:
  freeze: true
  warning: false
---

```{r}
#| label: Set up box storage directory

suppressMessages(library(tidyverse))
suppressMessages(library(glue))
PRE = "/Users/saideepgona/Library/CloudStorage/Box-Box/imlab-data/data-Github/Daily-Blog-Sai"

## COPY THE DATE AND SLUG fields FROM THE HEADER
SLUG="diagnose_training_tracks_issue" ## copy the slug from the header
bDATE='2023-09-20' ## copy the date from the blog's header here
DATA = glue("{PRE}/{bDATE}-{SLUG}")
if(!file.exists(DATA)) system(glue::glue("mkdir {DATA}"))
WORK=DATA

```


#todo

exact check of ref prediction coordinates (rerun enformer)

slight misalignment of aracena/ref?

Find basenji sequences with a TSS for checking correspondence of training data

Check if liftover maintains length