[maker-devel] Using GlimmerHMM with MAKER

[Shaun Jackman]

That worked! Thanks again, Carson.

A note for the record: I found that keep_preds=1 carries forward
pred_gffannotations, but not
model_gff annotations when that GFF file uses match and
match_partannotations (like a munged GlimmerHMM GFF file), which makes
sense I guess
now that I think about it.

Cheers,
Shaun


On 10 April 2014 14:35, Carson Holt <carsonhh at gmail.com> wrote:

> 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.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>
>
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