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hms-dbmi / chromoscope

Interactive multiscale visualization for structural variation in human genomes
https://chromoscope.bio/
MIT License
60 stars 6 forks source link

Can I use reference genomes from other species? #124

Open karen916 opened 9 months ago

karen916 commented 9 months ago

Dear Chromoscope Software Developers,

Greetings!

I have been utilizing your software and noticed that the reference genome selection seems to be limited to hg19 and hg38. May I inquire if your software supports the incorporation of other species' reference genomes provided by the user for plotting purposes? Additionally, I would like to know if the software can still perform the plotting correctly if I only provide a BEDPE file without supplying a CNV file?

I look forward to your response and would like to express my appreciation for developing such an excellent tool.

Best regards.

dominikglodzikhms commented 7 months ago

Hi Karen, at this point, only hg19 and hg38 are supported, but we are looking into adding more.

May I ask what species you would like to include? Do established reference genomes exist for these yet?

Currently the CNV file IS required, but we are working on removing this requirement and will deploy shortly. In the meantime, you could use an empty CNV file.

Thank you Dominik