[maker-devel] Maker: Re-annotation

[Carson Holt]

The option in trinity is --jaccard_clip
--> http://trinityrnaseq.sourceforge.net/#jaccard_clip

--Carson


From:  Innocent Onsongo <onson001 at umn.edu>
Date:  Tuesday, 21 May, 2013 11:58 AM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Maker: Re-annotation

Maker Development Team,

I am trying to use Maker for re-annotation using  gene predictions from
Augustus. We had previously used Augustus for gene prediction but now want
to combine these annotations with some EST data. I updated fields
maker_opts.ctl  as below

genome=CGS01058.fasta #genome sequence file in fasta format
est_gff=EST2Scaffold.gff3 # ESTs mapped to CGS01058.fasta using BLAT
pred_gff=Augustus.gff3 #ab-initio predictions from
other_gff=Promoters.gff3 #promoter annotations
other_gff=CpG_Islands.gff3 # CpG island annotations

Maker runs to completion and according to the log file annotation was
successful. However, it also gives a "Segmentation fault (core dumped)"
message. It does produce a GFF3 file but when I load the GFF3 file into IGV
and look it does not contain any of the exon definitions in Augustus.gff3.
Am I missing something?

Regards, 
Getiria

-- 
Getiria Onsongo, Ph.D.
Informatics Analyst, Research Informatics Support System
Minnesota Supercomputing Institute for Advanced Computational Research
University of Minnesota
Minneapolis, MN 55455
Phone: 612-624-0532
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