Quantcast
Channel: Post Feed
Viewing all articles
Browse latest Browse all 3764

Bedtools genomecov to identify regions at any coverage

$
0
0

Hi,

 

Is it possible to use bedtools genomecov with both -bga and -max flags?

I've been trying to do this (code below), but my resulting output isn't binned.

bedtools genomecov -max 1 -bga -ibam input.bam -g hg19.genome > output.bed

chr1  0       554304  0
chr1  554304  554309  5
chr1  554309  554313  6
chr1  554313  554314  1

Whereas I'd like it to be:

chr1  0       554304  0
chr1  554304  554314  1

Any help is much appreciated.

 

SB :)


Viewing all articles
Browse latest Browse all 3764

Trending Articles