---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
layout: post
title: Data Wrangling - CEABIGR C.virginica Exon Expression Table
date: '2023-04-05 07:02'
tags: 
  - data wrangling
  - Crassostrea virginica
  - CEABIGR
  - exon
  - ballgown
categories: 
  - 2023
  - CEABIGR
---
As part of the [CEABIGR project](https://github.com/sr320/ceabigr) (GitHub repo), Steven asked that I [generate an exon expression table](https://github.com/RobertsLab/resources/issues/1609) (GitHub Issue) where each row is a gene and the columns are the corresponding exons, filled with their expression value. For this, I planned on using the read count from the `ballgown` `e_data.ctab` files as an expression value.

Although the final code in the repo (linked in [RESULTS](#results)) is nice an tidy, it was generated through days and days of "fighting" with ChatGPT. Had to go through many rounds of trying ChatGPT to get this task accomplished. I was finally successful in getting ChatGPT to generate functional code by narrowing the scope of the work and sepcifying specific tools to use (i.e. `bedtools`) instead of relying on ChatGPT to select the correct tools on its own.

---

# RESULTS

Output folder (GitHub repo directory):

- [`ceabigr/output/19-exon-expression`](https://github.com/sr320/ceabigr/tree/main/output/19-exon-expression)

  #### Exon expression file

  - [S12M-exon_expression.tab](https://github.com/sr320/ceabigr/blob/main/output/19-exon-expression/S12M-exon_expression.tab?raw=true) (~52MB)

