Question: How many reads cover the exon per gene from a BAM? The gene (or exon) is totally covered by BAM file?
gravatar for Andrea Spinelli
14 months ago by
Andrea Spinelli10 wrote:

Hi! I want to calculate a percent of coverage (or the read count witch cover it) of the exons that code for a gene. How can I do? Which is the pipeline? Is it possible to get this information starting from the BAM file?

I'll like to get a result that seems like this:

chr | start | end | reads | exons | gene_name | percent_of_coverage

I would like to use python tools

Thanks a lot


coverage bam gene • 509 views
ADD COMMENTlink modified 14 months ago by Devon Ryan91k • written 14 months ago by Andrea Spinelli10
gravatar for finswimmer
14 months ago by
finswimmer12k wrote:

Hello Andrea,

if you don't want to reinvent the wheel have a look at picard CollectHsMetrics with the PER_TARGET_COVERAGE parameter. The output looks pretty much as you like to have it.

fin swimmer

ADD COMMENTlink written 14 months ago by finswimmer12k
gravatar for Pierre Lindenbaum
14 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum122k wrote:

see How to calculate average depth for each Amplicon in targeted amplicon sequencing?

ADD COMMENTlink written 14 months ago by Pierre Lindenbaum122k

Thank you Pierre, but I don't know which is the bed file for matching.

ADD REPLYlink written 14 months ago by Andrea Spinelli10
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