As part of the CEABIGR project (GitHub repo), Steven asked that I generate an exon expression table (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) 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-expressionExon expression file
- S12M-exon_expression.tab (~52MB)