Question: Per Base Coverage
0
gravatar for Info_Nowise
3.3 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 3.3 years ago by Info_Nowise10
4
gravatar for Aaronquinlan
3.3 years ago by
Aaronquinlan8.7k
United States
Aaronquinlan8.7k wrote:

Also,

bedtools coverage -abam aln.bam -b regions.bed -d
ADD COMMENTlink written 3.3 years ago by Aaronquinlan8.7k
2
gravatar for Zev.Kronenberg
3.3 years ago by
Zev.Kronenberg9.2k
United States
Zev.Kronenberg9.2k wrote:

samtools depth your.bam

ADD COMMENTlink written 3.3 years ago by Zev.Kronenberg9.2k
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