Question: how to find the amplified region from aln.bam file
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gravatar for trisha
19 months ago by
trisha10
India
trisha10 wrote:

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.

mi-seq paired end amplicon • 556 views
ADD COMMENTlink written 19 months ago by trisha10

If these are amplicons then you should already know what region was supposed to be amplified.

ADD REPLYlink written 19 months ago by Devon Ryan90k

I have not received the information about amplified region, that is in deed the task to find the amplified region.

ADD REPLYlink written 19 months ago by trisha10

If it is only one region...just visualise it in IGV

ADD REPLYlink written 19 months ago by YaGalbi1.4k

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.

ADD REPLYlink modified 19 months ago • written 19 months ago by Devon Ryan90k
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