Nanopore dRNA - view unmapped segments of mapped reads

Question

[yryan]

I've got some nanopore directRNA reads and I'm trying to extract the portions of these reads that are 5' and 3' of my reference genes. Is there an easy way to do so? I'm looking for something like samtools view -f4, except I want to view the umapped segments of my mapped reads.

So far I've aligned them to my references, but can't find a way in my genome viewer to view outside of the reference.

Thanks for any help!

Answer 1

[GenoMax]

IGV has a setting that you can turn on to see clipped/unaligned data.

[yryan]

Ahh thats worked, thanks!