[maker-devel] final annotation issues

[Carson Holt]

I would not recommend single-exon=1 unless this is an organism where you expect a lot of single exon genes (typically fungi or oomycetes).  It’s best to review models visually in something like Apollo to see how evidence alignments compare to gene predictions. There is always the chance that you have some overmasking that could trim some regions you don’t want to lose.

—Carson



> On Apr 3, 2020, at 11:02 AM, shore at yorku.ca wrote:
> 
> Dear Maker team,
> 
> I believe we are the final stage of annotation of a plant genome, having
> previously trained snap following 3 rounds.
> 
> In our attempts at final annotation we have now added new transcriptome data,
> and generated a repeat library for our species (so we now mask with that, as
> well as database of plant repeats , and TE proteins).
> 
> In this final annotation run, we've set keep_pred=1 and then plan to
> screen the final gff file retaining sequences with AED<= 0.5 (or there
> abouts) and ones that possess a pfam domain .
> 
> I've compared some of the proteins obtained in our previous round of Maker with
> the latest. Indeed the masking appears to have removed some that were TEs. A
> number of proteins differ somewhat, likely the result of different intron/exon
> boundary calls, and some are quite different in length.
> In particular some are roughly twice the length in previous annotation, and
> appear to be of the correct size previously , based upon online blasts.
> 
> It is this latter finding that I'm concerned about.
> Why it has occurred.
> 
> I did set single-exon=1 and wonder if that is causing this effect?
> 
> Thanks and sorry for the long-winded email.
> 
> Joel
> 
> 
> 
> -- 
> Dr. Joel S. Shore
> Prof. Biology
> York University
> 
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