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Custom genomes #95
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Hi @Zhuxitong, thanks for your interest in chimeraviz 🙏 Currently chimeraviz is hardcoded to only allow hg19 and mm10, as you've seen. You can see this here:
It seems to me that to support a custom genome, then at least those places in the code would need to be updated.
Those are my initial thoughts. I do not have time to implement anything like this myself, but would very much welcome a pull request with the change. |
Hi, @stianlagstad, Thanks for your suggestions in great details. During last week, I tried to modify those source codes, but I could only make get_circle working by creating a fake band file and modifying the codes you referred. I failed to run other functions mainly beacuse of the lack of ensembl db file. I also tried to make a custom db file, but couldn't find an easy way. I think there should be a way to expand the scope of using chimeraviz by solving this problem, and I will try again. So better leave this Issue open :) |
Hi, @stianlagstad !
I would like to know if there is a way to make a custom genome database, such as plant genomes, and then feed to import_jaffa with a new parameter?
I saw you have added mm10 since initial human genome. I thought with genome/transcript fasta and corresponding gff annotation file, we can make a database for any species.
It would also be great if you can provide me some suggestions like where I need to start and what fucntions I should modify. I may try myself then.
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