Promoter beds extend the genome size

[dariarom94]

Last promoter on chrM for me was out of the chormosome size

[sreichl]

Do you mean some promoter regions extend beyond the respective chromosomes?

This probably results from the extension left & right from the gene's start site.
If yes, I should add here not only a check for the start of the region but also a check for the end:

atacseq_pipeline/workflow/scripts/get_promoter_regions.py

Line 15 in 269271e

# Ensure start is not negative

[dariarom94]

Exactly! I believe that bedtools slop with chromSizes would solve it :)

[sreichl]

do you mean instead of the manual -/+ calculation I should just use bedtools' slop?

[sreichl]

fixed now, comparison between old and new showed this results (for mm10). Was that your case?

→ diff promoter_regions.bed promoter_regions_old.bed 
51206c51206
< chrM  14922   16299   ENSMUSG00000064372
---
> chrM  14922   16422   ENSMUSG00000064372