parameter usage for RNA sequencing samples

[mahwish2]

Hi, I have multiple bam files (test1.bam test2.bam test3.bam) and the genome fasta and annotation gff.
I want to visualize it with jigv. Could you please post the command for this.

Thanks

[mahwish2]

When I simply try to use the following:

jigv
--fasta xxx.fa
--sites xxx_full.bed
/path/jigv/*.bam > regions.html

I get the following error:
Error: unhandled exception: /home/brentp/src/jigv/jigv.nim(376, 12) found.len == 1 [jigv] found {} sample names (SM read-group tags in bam header), expected exactly one. [AssertionError]

Also to mention, I am not sure about --sites parameter, since in my case I am not interested in particular region.

Thanks

[brentp]

hi, jigv expects your bam files to have proper read-groups, it seems that's not the case.
those allow jigv to get the sample name.