Question: Per Base Coverage
0
gravatar for Info_Nowise
2.1 years ago by
Info_Nowise10
Info_Nowise10 wrote:

Is there a way to obtain per-base coverage for a define chromosome interval using a bam file generated from Illumina single-end reads? genomeCoverageBed in Bedtools does not seem to have an option for it.

ADD COMMENTlink written 2.1 years ago by Info_Nowise10
4
gravatar for Aaronquinlan
2.1 years ago by
Aaronquinlan7.3k
Aaronquinlan7.3k wrote:

Also,

bedtools coverage -abam aln.bam -b regions.bed -d
ADD COMMENTlink written 2.1 years ago by Aaronquinlan7.3k
2
gravatar for Zev.Kronenberg
2.1 years ago by
Zev.Kronenberg7.5k
United States
Zev.Kronenberg7.5k wrote:

samtools depth your.bam

ADD COMMENTlink written 2.1 years ago by Zev.Kronenberg7.5k
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