[maker-devel] Question on post processing of annotations

[John Cornelius]

I'll look into that thanks. I had been previously just been looking for
things in regards to the script itself and its functionality.

On Fri, Jan 22, 2016 at 3:01 PM, Carson Holt <carsonhh at gmail.com> wrote:

> 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
>
> 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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>
>
>


-- 
John Cornelius
MCB PhD Candidate
Arizona State University
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