[maker-devel] Using GlimmerHMM with MAKER

[Carson Holt]

keep_preds=1 will force MAKER to keep ab initio results even if their is no
evidence supporting them.

--Carson


From:  Shaun Jackman <sjackman at gmail.com>
Reply-To:  Shaun Jackman <sjackman at gmail.com>
Date:  Thursday, April 10, 2014 at 3:32 PM
To:  Carson Holt <carsonhh at gmail.com>
Cc:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] Using GlimmerHMM with MAKER

Thanks, Carson. That helps. I'm trying to do a completely ab initio gene
annotation without any est or protein homology evidence, at least for now.
The GFF file produce by maker is empty. How do I carry the GlimmerHMM
pred_gff (or model_gff) annotations through to the end? Ultimately, I'd like
to merge annotations from multiple ab initio predictions.

Cheers,
Shaun


On 10 April 2014 11:53, Carson Holt <carsonhh at gmail.com> wrote:
> Make sure it's not GTF or GFF2, but if it is GFF3 You can substitute match for
> mRNA and match_part for CDS.  Then it will be interpreted as a two level
> alignments feature which can be given to pred_gff.
> 
> --Carson
> 
> From:  Shaun Jackman <sjackman at gmail.com>
> Reply-To:  Shaun Jackman <sjackman at gmail.com>
> Date:  Thursday, April 10, 2014 at 12:34 PM
> To:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
> Subject:  [maker-devel] Using GlimmerHMM with MAKER
> 
> The GlimmerHMM gene prediction software outputs a GFF file that includes mRNA
> and CDS features, but it does not include gene or exon features, and so it
> does not appear to be working with MAKER. Has anyone else used GlimmerHMM with
> MAKER, and how did you deal with this issue?
> 
> Cheers,
> Shaun
> _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/mak
> er-devel_yandell-lab.org



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