[maker-devel] Using GlimmerHMM with MAKER

[Carson Holt]

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20140410/f5e9bd25/attachment-0003.html>