PASA annotation update: CDS feature phase wrong

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Saravanaraj Ayyampalayam

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Feb 16, 2016, 5:09:43 PM2/16/16

to pasapipeline-users

Hello,

I am using PASA annotation compare/update to add UTR and alt splicing info to my genome annotation. The original annotation was produced by EVM and passes gff validation by the latest genome tools gffvalidator. The updated annotation fails to pass the gffvalidator test. The error is "CDS feature on line xxxx in file "yyyyy.gff3" has the wrong phase 2 (should be 1)".

In the updated annotation file, the genes marked as "ORIGINAL: .... not modified by PASA" has a different phase for its CDS features compared to the original annotation. The difference seems to be only in the CDS features with phase as 1 or 2 in the original annotation. (1 is changed to 2, and 2 changed to 1).

The PASA updated gene models all seem to have the correct phase for their CDS feature.

I am just wondering if others have seen this and is there an faster way to fix it rather than hand edit the annotations?

Thanks,

-Raj

Brian Haas

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Feb 16, 2016, 5:16:14 PM2/16/16

to Saravanaraj Ayyampalayam, pasapipeline-users

Hi Raj,

It sounds like we need to update EVM so that it produces the correct phase info.

In PASA, you'll find a utility that will update all the phase info:

PASA_HOME/misc_utilities/gff3_phase_generator.pl

usage: ./gff3_phase_generator.pl gff3_file genome_db > updated.gff3

Let's see if that works for you.

best,

~brian

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