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vgteam / sequenceTubeMap

displays multiple genomic sequences in the form of a tube map
MIT License
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How to visualize a gbz file #317

Open leone93 opened 1 year ago

leone93 commented 1 year ago

Sorry guys, I'm trying to visualize the output of a my cactus pangenome analysis using sequenceTubeMap but it is not straightforward to do it. I would like to visualize the gbz files but, even if I modified the config.json to let my put to be able to be in the mounted files, I cannot visualize any change in the interface. And it is asking me a bed files in the web interface, not even a gbz, gfa or vg. Frankly I don't understand how it work from you instructions. Thanks

adamnovak commented 1 year ago

I think #318 will help with this. I think you want to put the files in exampleData, go to custom (mounted files) mode, hit Configure Tracks, and hit + in that dialog for each file you want to use. If you want the haplotypes from a GBZ you need to add it in there twice: once as a graph and once as haplotypes.

Does that help?

dmgood11 commented 1 month ago

I would add that I haven't been able to visualize the .gbz files produced by minigraph-pangenome in sequenceTubeMap. This is a relatively small graph (15kb slice from 12 genomes). I've only been able to visualize the .vg files that are output into the chrom-alignments subfolder of m-p's output dir. Is there some preprocessing of .gbz files that is necessary for them to be visualized directly in sequenceTubeMap?