Counting number of reads in my peak file
2
0
Entering edit mode
7.4 years ago
ChIP ▴ 590

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

ChIP-Seq Bamtools Python • 4.8k views
ADD COMMENT
1
Entering edit mode
7.4 years ago

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.

ADD COMMENT
1
Entering edit mode
7.4 years ago
Ming Tang ★ 2.7k

Or featurecount

ADD COMMENT

Login before adding your answer.

Traffic: 1970 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6