interpreting inversions on IGV

Question

[Shaghayegh]

I just started working with PacBio and Nanopore long reads, after some preliminary QCing I mapped the reads using minimap2.

I am looking at the inversions for now and I have igv images for one of my regions. I want to know is it how I should expect to see the inversions on IGV? I do not understand whether the gaps are oK or should I expect the reads below the gaps or should I expect to see them filling the gaps? Thanks for any help interpreting it.

Answer 1

[cmdcolin]

you may be able to turn on a setting "Link supplementary alignments" to show multiple segments of the alignment as a single, continuous row, with the inversion in the middle. in the SAM format, the inversion is likely split into e.g. 3 lines for a long read that goes through the whole inversion, one line is e.g. forward, one like is reverse, and then the other is forward, and one of the lines will be marked as primary (no flag 2048) and the other two will be marked as supplementary (flag 2048) and they will all share the same read name and have an SA tag linking them

see https://www.pacb.com/blog/igv-3-improves-support-pacbio-long-reads/

[Shaghayegh]

Thanks a lot, very helpful. I activated "linked supplementary alignments" and can see gaps are filled.