Identify transcripts from genome positions

Question

[jomiles26]

Hi,

I have a large list (20,000+ rows) of C. elegans genomic positions in three columns: chromosome, start position and end position.

Does anyone know how I can identify which transcripts (if any) overlap with each position?

Thanks!

Answer 1

[lieven.sterck]

Sounds like a job for bedtools, more preciously bedtools intersect

have you looked into that?

[jomiles26]

I haven't used bedtools before, I'll look into it. Thanks