[maker-devel] Question on post processing of annotations

[Carson Holt]

Hi John,

Do you mean the match/match_part features that are source snap_masked? Those are not genes, they are reference alignments representing the ab initio SNAP calls, and it would be incorrect to rename them.  They do not have a 1 to 1 relationship with the final gene models.  Sometimes a gene model will overlap 2 or more uninformed SNAP ab initio reference alignments, or one SNAP reference alignment may overlap multiple final gene models, so names cannot just be passed from one to the other.

If you want to add specific SNAP models to the final annotation set, you would need to upgrade them to being a gene/mRNA/exon/CDS feature before you can do that. You can do that with manual editors like Apollo, or you can supply a subset of the features you want to upgrade to maker in the pred_gff= option as a separate run, put existing models in model_gff=, and run with keep_preds=1.

I know I have covered this previously in greater detail as part of the devel list. If you search the archives for the keywords pred_gff, keep_preds, and iprscan you should come across a number of threads that may be helpful —> https://groups.google.com/forum/#!forum/maker-devel <https://groups.google.com/forum/#!forum/maker-devel> 

Thanks,
Carson



> On Jan 22, 2016, at 2:38 PM, John Cornelius <jcornel3 at asu.edu> wrote:
> 
> Hi, I'm using the maker_map_ids script to change the gene ids on an annotation that I just finished. However, I noticed that it does not change the name of genes predicted by SNAP. Is there any way to include SNAP genes for consideration by maker_map_ids? Thanks.
> 
> -- 
> John Cornelius
> MCB PhD Candidate
> Arizona State University
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