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im3sanger / dndscv

dN/dS methods to quantify selection in cancer and somatic evolution
GNU General Public License v3.0
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calculation of dn/ds for bacterial genome data #98

Closed chantisakee closed 1 month ago

chantisakee commented 1 month ago

Hi,

Thank you for your interesting tool! :) I'm interested in calculating dn/ds for rickettsia sequencing data and i can't find a table of transcripts of this spp. from Ensembl BioMart. I'm wondering how can i generate a RefCDS object with another dataset like gtf file?

Thank you so much,

im3sanger commented 1 month ago

Hello,

Thanks for your interest in dndscv. Since bacterial genes do not have introns, the input annotations are very simple to adapt from other sources, including gtf. Please see this previous reply to see if it answers your query: https://github.com/im3sanger/dndscv/issues/62

Best, Inigo

chantisakee commented 1 month ago

Thanks a lot! That is really helpful.