Find the number of mapped Reads

Question

[Valeria]

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?

[Valeria]

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!

[Valeria]

I need to use Bedtools utilities

[WouterDeCoster]

Why? The only reason I can think of is "because it's a homework question".

[GenoMax]

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.

Answer 1

[GouthamAtla]

http://bedtools.readthedocs.io/en/latest/content/tools/multicov.html

http://www-huber.embl.de/users/anders/HTSeq/doc/count.html

http://bioconductor.org/packages/release/bioc/html/DEXSeq.html

http://bioinf.wehi.edu.au/featureCounts/