Can IGV tell me where to look?
Hopefully that is a dumb question!
I have Nanopore MinION reads from a (dirty) PCR and I am looking at my hg38-alignment on IGV.
Can IGV somehow tell me where to look for reads/coverage? For example at the level of a chromosome. I do not understand how I am supposed to visually scan for reads/coverage.
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francois •
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You need to zoom in enough (choose a chromosome) and then start looking for read outlines to show up. You could also run
qualimapon your BAM file to get an overview of alignment stats which includes coverage graphs.I think you should have a look at
samtools viewwhich will tell you where reads are. If that's too much information you could try bedtools genomecov