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Published 20 hours ago • verified publisher icon dib-lab

include BUSCO hits in gff3

Open macmanes opened this issue 8 years ago • 2 comments

Camille,

I want to retain all contigs for which any annotation data exists, including BUSCO hits. This would be easy if the BUSCO results were including in the final gff3 file in some way. What do you think about including them?

macmanes avatar Jun 07 '16 15:06 macmanes

I definitely support it. Do you have ideas on how to represent these in the gff3? The standard really demands having start/end coordinates for each feature; I suppose I could just have the features span the entire transcript (which seems kludgy/inaccurate), or pull coordinates from the BLAST or hmmer outputs. What do you think?

camillescott avatar Jun 08 '16 22:06 camillescott

Been looking into this. The output from BUSCO is very raw -- many hits per BUSCO, sometimes multiple per transcript, combined from both hmmer and tblastn. I think the short term solution for 1.0 will just be to set the start and end as the start and end coordinates of the transript, and think about dealing with it more intelligently later.

camillescott avatar Oct 20 '16 23:10 camillescott