Question: how to calculate the coverage over a specif coordinate
2
gravatar for Lila M
3.3 years ago by
Lila M 860
UK
Lila M 860 wrote:

Hi everybody, I have bam files for RNAseq, and I know the coordinates for specific exons of interest. I would like to know if there is any way to overlap my bam files over those specific coordinates and get the coverage for those regions. I usually use bedtools coverage, but to compare between samples. I was wondering if I can create a bed files with my coordinates and do:

bedtools coverage -a my.bam -b mycoordintes.bed -s

will that work?

Many thanks!

rna-seq coverage exon • 2.8k views
ADD COMMENTlink written 3.3 years ago by Lila M 860
1
gravatar for Medhat
3.3 years ago by
Medhat8.8k
Texas
Medhat8.8k wrote:

you should use -abam

for eexample:

bedtools coverage -abam sorted.bam -b regions.bed.gz | grep ^all > mycoverage.tab
ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by Medhat8.8k
1

what about?

java -jar GenomeAnalysisTK.jar -T DepthOfCoverage -R [reference fasta] -I [bam file] -L [bed file]

which one is better?

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by Lila M 860
1

I think they both do the same job

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by Medhat8.8k
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