how to find the amplified region from aln.bam file
I have received mi-seq data for targeted genomic region of human. I need to find the amplified region. How could I find from my .bam file or .bed file which region is the amplified region (as position in .bam file). Also from the coverage studies I found that some reads have very less coverage where as a few with very high coverage. what could be the reason behind it.
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If these are amplicons then you should already know what region was supposed to be amplified.
I have not received the information about amplified region, that is in deed the task to find the amplified region.
If it is only one region...just visualise it in IGV
I rather doubt someone thought to themselves, "hey, I just found some random primers, let's some PCR, see if I get a product and pay to sequence it if there is one!" That'd be a complete waste of money. Either someone is wasting your time or you're omitting important details.