Can IGV tell me where to look?

Question

[francois]

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.

[GenoMax]

You need to zoom in enough (choose a chromosome) and then start looking for read outlines to show up. You could also run qualimap on your BAM file to get an overview of alignment stats which includes coverage graphs.

[WouterDeCoster]

I think you should have a look at samtools view which will tell you where reads are. If that's too much information you could try bedtools genomecov