[maker-devel] Alternative Splicing and ipr_update_gff

[Jason Gallant]

Hi Everyone,

Doh!  Very stupid error— I ran my interpro scan on the augustus masked
proteins file instead of the maker masked proteins file by mistake.

Apologies!

Jason Gallant

On Fri, Nov 13, 2015 at 3:03 PM Jason Gallant <jgallant at msu.edu> wrote:

> Hi Everyone,
>
> Another nitty gritty question, probably directed at Carson once more.
>
> I decided to make one more go at my maker annotation, this time turning on
> alt_splice=1.   I have been keeping keep_preds=1 on to export the “max”
> dataset as detailed in Campbell et al (2014), with the hopes of “rescuing”
> genes that have IPR domains do not have evidence.
>
> Everything works swimmingly when alt_splice=0, but when activated, the run
> behaved normally— I ran gff3_merge and fast_merge to obtain proteins and
> transcripts, and found that as predicted the resulting fasta files
> contained more proteins than the initial run.
>
> I ran IPR scan and now am trying to update my GFF3 file to obtain the
> “maker standard” dataset— what I am noticing is a sudden complaint by the
> ipr_update_gff script about use of an uninitialized value.
>
> This appears to have happened to others:
> https://groups.google.com/d/msg/maker-devel/dM4WvyghYks/BboRZQLmEF8J
>
> And indeed, I can verify that the first protein listed in my fasta file is
> only listed as “augustus_masked”  match/match part in the original GFF3
> file.
>
> If I understand the ipr_update_gff script correctly, this transcript will
> be ignored because it lacks the mRNA type.  Is this expected naming
> behavior for the alternative splicing?  I would have expected the
> alternative splice variants to be listed as alternative mRNAs under the
> same parent gene?  Is there some sort of misconfiguration or am I expecting
> incorrectly?
>
> Hopes for any help you all can provide in diagnosing
>
> Best,
> Jason Gallant
>
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