Hi,

I need some advise on calculating coverage

Basically for a set of BAM files, WGS, WES and RNA-Seq - I am interested in calculating and representing coverage - to show the contrast between these differing sequencing techniques (and limited to that ... not comparison). The coverage needs to be calculated at gene/exon level.

I am comfortable enough with determining the region of interest and extracting those regions from NCBI's Refseq.

However, I would appreciate some guidance around various coverage metrics for WGS, WES and RNA-Seq and what characteristics and limitations they have.

Needless to say, I am willing to do the background reading - but some guidance in this matter will help me understand the landscape.

Thanks, Himanshu