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Pangenome presence absence viz ? #1641
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It would definitely be great to add pangenome "presence absence" (PAV) visualizations one option would be converting your data format from TSV to VCF so that https://github.com/elsiklab/multivariantviewer could interpret that way you can keep multi-column as you mentioned, you could also make a sort of 'binary bedgraph/bigwig' for each sample, and use e.g. multibigwig for that we also had a user that was looking at PAV and used https://github.com/cmdcolin/jbrowse_piechart |
Great, thanks for those tips. The piechart one is very new for me. I think I'll try the bedgraph one first, but what do you mean by Is there a JBrowse1 multibigwig component, or do you mean for creation of bigwig files ?
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Dear devs,
I'm interested in visualizing a pangenome matrix from odgi pavs in JBrowse1.
Maybe someone has made something like this viewer, panache as an example.
https://www.appliedbioinformatics.com.au/wheat_panache/
I think it might be possible using a bedgraph -> bigwig conversion, and then individual customized tracks with low track height, eg 50px. But could something more elegant be done ?
For example the below matrix would be represented by 3 separate bedgraphs/bigwigs, each containing the binary presence absence data in the last 3 columns.
Input format tsv input example (more at https://odgi.readthedocs.io/en/latest/rst/tutorials/presence_absence_variants.html )
Thanks,
Colin
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