This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to merge gff files deriving from several evidences

Hi, I'd like to understand which methods are useful for merging gff3 files deriving from different evidences.

When I run EvidenceModeler, it underestimates, and I have a BUSCO result lower than the single evidence.

Thanks,

Marco

evidencemodeler merge gff gff3 annotation
• 2,617 views • link
updated by Mike • Mike • written by marco.sollitto • marco.sollitto

Whar do you mean by "I have a BUSCO result lower than the single evidence"?

• 0 views • link
written by Juke34 Juke34

hey Marco, what did you end up using? Id love to hear, thanks.

• 0 views • link
written by Mike • Mike

1 answer

I like the tools GffRead and GffCompare. The later can give you a lot of information when comparing different GFF or GTF files that might point you in the right direction.

• 0 views • link
written by Trivas • Trivas

I have tried both of them, but a lot of "duplicates" still remain. Through these tools, I reach a % of complete BUSCO ~93% (40% of "duplicates").

My genome has a ~98% of Complete BUSCOs%.

• 0 views • link
written by marco.sollitto • marco.sollitto

When computing BUSCO on annotation you must remove isoforms to avoid to over-estimate "duplicates"

• 0 views • link
written by Juke34 Juke34

Yep, I know about different isoforms, but, in the file there are still several hits deriving from different evidences (with some nucleotides of difference, so no real isoforms, but only low accuracy in gff annotations).

• 0 views • link
written by marco.sollitto • marco.sollitto

This is normal, most often annotations have lower BUSCO score than the assembly

• 0 views • link
written by Juke34 Juke34

Log in to answer this question.

More posts like this