Entering edit mode
7.8 years ago
Valeria
▴
10
Hello! I have two file, one with sorted reads(bam) and another with the exons(gft). I want to find the number of reads that are mapped in the set of exons intervals with bedtools. How can I do this?
Yes, it is a project for bioinformatics course! However at the end I used:
intersectBed -abam sorted_reads.bam -b myfile.gtf| coverageBed -counts -abam stdin -b Imyfile.gtf>FINAL
Thanks everybody for the help!
I need to use Bedtools utilities
Why? The only reason I can think of is "because it's a homework question".
Bedtools hint is included by @Goutham below. You must do some work yourself (read the manual page or search Biostars) to put together the necessary command line.