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brentp / jigv

igv.js standalone page generator and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"
MIT License
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parameter usage for RNA sequencing samples #15

Open mahwish2 opened 3 years ago

mahwish2 commented 3 years ago

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 commented 3 years ago

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 commented 3 years ago

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.