Question: How many reads cover the exon per gene from a BAM? The gene (or exon) is totally covered by BAM file?
0
gravatar for Andrea Spinelli
9 months ago by
Italy/Pisa
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

Andrea

coverage bam gene • 333 views
ADD COMMENTlink modified 9 months ago by Devon Ryan88k • written 9 months ago by Andrea Spinelli10
2
gravatar for finswimmer
9 months ago by
finswimmer11k
Germany
finswimmer11k 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 9 months ago by finswimmer11k
0
gravatar for Pierre Lindenbaum
9 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum118k wrote:

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

ADD COMMENTlink written 9 months ago by Pierre Lindenbaum118k

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

ADD REPLYlink written 9 months ago by Andrea Spinelli10
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