Counting number of reads in my peak file

Question

[ChIP]

Hi!

The map function from bedtools can help in generating reads per peak for a given peak file.

But how can I get number of reads per peak (for a given peak file) from a Bam file.

Does anybody has some quick and dirtty solution for this :) and is willing to share :)

Thank you

Answer 1

[dariober]

Maybe bedtools coveragebed lijke:

coverageBed -abam aln.bam -b peaks.bed -counts > peaks.cnt.bed

Your peak file, peaks.bed, should be in bed format.

Answer 2

[Ming Tommy Tang]

Or featurecount