NGS - Mapping quality of specific regions

Question

[dominik.saburo]

I have a problem with estimation which gene exons are well mapped. I discovered that there is a software which is called Qualimap but I think it only shows me the quality of mapping in comparative with whole genome and the score is only in percentage.

In my reasearch I have a specific ngs gene panel for Osteogenesis Imperfecta and we have there 28 genes. I was checking which exon is well mapped by IGV software but it is taking so much time to check all the exons in all genes in all of my patients.

So the main question is :How can I see which exons are mapped or not in more simpliest and faster way?

[GenoMax]

featureCounts is another option but will only provide counts (not "quality" - title of your post does not fully match the question).

Answer 1

[Tom_L]

I did that few days ago using bedtools coverage (http://bedtools.readthedocs.io/en/latest/content/tools/coverage.html).

Give it a BED files (containing your exons) as -a and your BAM file as -b with and it will tell you how many reads are mapped to each exon (-counts argument).

[dominik.saburo]

This is it! Thanks for help!