How many reads cover the exon per gene from a BAM? The gene (or exon) is totally covered by BAM file?

Question

[Andrea Spinelli]

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

Answer 1

[finswimmer]

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

Answer 2

[Pierre Lindenbaum]

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

[Andrea Spinelli]

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