I am currently work on WGS data in galaxy.org and I want figure out how to run circos in correct manner. I have a alignment vcf files, reference genome files. How I convert these files into the circos configuration files? what are the necessary materials for that?
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I was stuck in the steps of making karyotype file for circos. when I run the circos all the time it gives me error. what are possible tools that I can use for this
Hi @E.L.A.T_LIYANAGE
Maybe check information on CIRCOS site:
https://circos.ca/documentation/tutorials/ideograms/karyotypes/
CIRCOS provides built-in karyotype data for some assemblies.
If built-in data is not available for the species, you need info about chromosomes and bands. CIRCOS site suggests UCSC Genome Browser as source of information about karyotypes and bands. From quick look, UCSC GB provides data in different format, but it can be rearranged by column swap (cut columns tool in Galaxy). If you want karyotype and bands, as in the tutorial, create both parts separately and concatenate the final result. Maybe test both parts with CIRCOS before concatenation.
Kind regards,
Igor
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