[maker-devel] New assembly annotation

[Carson Holt]

Fewer transcripts can mean fewer split and spurious genes. It can also be bad merges because of overtraining.  Use BUSCO to evaluate the completeness of gene models rather than transcript count.  Also review models visually using something like Apollo.  You will be able to see if models are spanning distinct evidence clusters or if they were previously split within evidence clusters.  That will help you better identify if the models now better follow the evidence alignments.

—Carson


> On Apr 10, 2020, at 10:33 AM, andrei.kiselev at lrsv.ups-tlse.fr wrote:
> 
> Hello.
> I'have recently got a new genome assembly using PacBio of oomycete Aphanomyces. 
> I used MAKER in the manner as described here https://groups.google.com/forum/#!searchin/maker-devel/new$20assembly%7Csort:date/maker-devel/Xo5YbWgNwFw/KstkmXYYAgAJ <https://groups.google.com/forum/#!searchin/maker-devel/new%2420assembly%7Csort:date/maker-devel/Xo5YbWgNwFw/KstkmXYYAgAJ>
> 
> After first run I got the number of transcripts slightly higher than were in gff file of previous version of genome. Then I run the second MAKER with new gff file in option pred_gff + augustus trained for my species. As a result I got only half of the transcripts from initial gff.
> 
> Is there something that I could overlook running MAKER? Attached is control file of the last run.
> 
> Thank you in advance.
> Andrei
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