This is my scenario: I am doing whole genome amplification from human cells, and then doing NGS with an Illumina platform. I get bam files from the machine. I am trying to find out how many times the mitochondrial DNA is represented in each sample. I know that mitochondrial DNA gets amplified during my whole genome amplification (I confirmed with the manufacturer of the kit). I've gotten to the point where I downloaded IGV and can map the reads to the human mitochondrial genome. I can see the mapped reads. But I cannot figure out how to get a specific value, i.e. a count of the specific number of mapped reads in each sample. The idea is to be able to tell if one sample had more mitochondrial DNA than another sample.
I am working on a Windows 7 64-bit computer. (But could have access to a mac as well)
Thanks so much any help is greatly appreciated!