[maker-devel] Maker predicts way too few genes/proteins

[Carson Holt]

Make sure you are training either SNAP or Augustus and not just protein2genome or est2genome. You can also rescue rejected Augustus/SNAP models by running them through InterProScan and then giving any model that contains an InterPro domain to the model_gff= option.

BASIC PROTOCOL 5 from this protocols paper —> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286374/ <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286374/>

—Carson


> On Dec 3, 2021, at 1:35 PM, Adam Stuckert <stuckerta at gmail.com> wrote:
> 
> Hello,
> 
> I am working on annotating several different assemblies, but I am having difficulty getting a reasonable number of predicted genes/proteins. My annotations always predict way too few genes (thousands too few) in the final transcript/protein fasta files. So, I am seeking help.
> 
> My approach is to annotate with EST evidence from the same species (either straight from transcriptome assemblers or predicted coding regions from TransDecoder) and use protein evidence from uniprot + related species. Simple repeats are softmasked within Maker. All repeats are masked in Maker, and I am supplying a repeat library that includes lineage-specific repeats as well as species specific repeats that are modeled by RepeatModeler2. I am using Maker version 3.01.03. 
> 
> I'm attaching my options control file. Any help to troubleshoot this would be greatly appreciated.
> 
> Thanks,
> Adam
> 
> -- 
> Adam Stuckert
> 
> <maker_opts>_______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20220103/18c541bb/attachment-0002.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: smime.p7s
Type: application/pkcs7-signature
Size: 1376 bytes
Desc: not available
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20220103/18c541bb/attachment-0002.p7s>