search

vgteam / vg

tools for working with genome variation graphs
https://biostars.org/tag/vg/
Other
1.09k stars 193 forks source link

How to generate variants by RNA-seq using vg tools #3632

Open GeorgeBGM opened 2 years ago

GeorgeBGM commented 2 years ago

Hi Vg team,

I have a problem,I'm wondering if Vg tools can be used for variants(snp;indel;SV) call basing on bulk RNA sequencing. You known that the small variants can be detected based on RNA sequencing by GATK process, so if VG can be used for RNA sequencing similar to the analysis of DNA sequencing data?

A possible workable process is as follows, vg mpmap-->vg call(https://www.biostars.org/p/9514102/)

Do you have any good advice?Thanks.

Best,Du

jonassibbesen commented 2 years ago

Hi Du,

We do not have any experience running the vg call pipeline on RNA-seq data as far as I know. I am therefore not sure how well it would perform. For example the coverage differences due to expression might be a problem for vg call since I think it expects uniform coverage. However, there should not be anything keeping the pipeline for running on RNA-seq data. The only thing you need to keep in mind is that you would need mpmap to output single-path alignments (GAM). You can do that using this option: -F GAM

Best, Jonas

Sourirewang commented 2 years ago

Hi, Vg team, I’m @Sourirewang and I’m interested in vg tools.I just have two full-length transcriptome and many transcriptome sequencing data. And I wonder whether a pantranscriptome can be constructed without a reference genome? Thanks a lot if you can reply.