split gamp by chromosome or extract specific regions.

Question

[Juhyun]

Hi,

I am trying to run transcriptome analysis, but RPVG is failing. I suspect this could be due to some issues with tangled graphs, so I am attempting to run RPVG by chromosome or by using specific regions. However, I am unable to figure out how to split the GAMP file or extract specific regions from it. Could you please guide me on how to do that?

Thank you in advance for your help!

[Jordan M Eizenga]

As of this moment, there's not a very direct way to do this. With GAM files, it's possible to use vg annotate -b followed by vg filter -U -F. For a GAMP file, you could convert to a GAM and then do this process, but the conversion is lossy. However, you could extract the read names and then use vg filter -M -N.