[maker-devel] tbl2asn errors

[Carson Holt]

Very cool.  I'll try it out as well.

--Carson

From:  "Geib, Scott" <Scott.Geib at ARS.USDA.GOV>
Date:  Thursday, April 17, 2014 at 2:59 PM
To:  "Mack, Brian" <Brian.Mack at ARS.USDA.GOV>, "maker-devel at yandell-lab.org"
<maker-devel at yandell-lab.org>, "Brian Hall (bhall7 at hawaii.edu)"
<bhall7 at hawaii.edu>
Subject:  Re: [maker-devel] tbl2asn errors

Hi Brian, 
We have a tool to deal with this in development, you should not directly
upload your maker output to NCBI, you need to filter out genes, check that
things are sane, etc.
http://brianreallymany.github.io/GAG/
It is still in active development, first full release is planned for the end
of this month (if you can wait 1.5 weeks).  It has no dependencies and
maintains parent/child relationships (for example if you remove a gene, it
will also remove associated CDS/mRNA).  In a release planned for then end of
the month, you will be able to  perform functions like removing short
features, long features, flagging things for review, etc. It also generates
an updated genome.fasta file, gff3 file, and sequences files for
CDS/mRNA/peptide based on edits made.  Hopefully this is helpful to you.

Scott
 
---------- Forwarded message ----------
From: Mack, Brian <Brian.Mack at ars.usda.gov>
Date: Thu, Apr 17, 2014 at 10:34 AM
Subject: [maker-devel] tbl2asn errors
To: "     <mailto:maker-devel at yandell-lab.org> "
<maker-devel at yandell-lab.org>

Hi, I thought I would try asking my question here as NCBI was not able to
give me much assistance.  In preparation for submitting to NCBI, I converted
my my MAKER gff3 to NCBI tbl format using the gff32tbl script that Carson
posted a link to in this thread
(http://gmod.827538.n3.nabble.com/NCBI-feature-table-tt4040473.html#a4040475
). It seemed to have converted fine, however when I use NCBIs tbl2asn
program I get numerous errors in my errorsummary.val file:
 
     4 ERROR:   SEQ_FEAT.BadTrailingCharacter
   217 ERROR:   SEQ_FEAT.NoStop
   438 ERROR:   SEQ_FEAT.ShortIntron
   171 ERROR:   SEQ_FEAT.StartCodon
   171 ERROR:   SEQ_INST.BadProteinStart
   291 WARNING: SEQ_FEAT.NotSpliceConsensusAcceptor
   648 WARNING: SEQ_FEAT.NotSpliceConsensusDonor
   118 WARNING: SEQ_FEAT.ShortExon
 
In addition, all of the genes, cds, and mRNA coordinates in the resulting
sqn files are decreased by one. For example my tbl file will have gene
coordinates of 440869 – 441931, but the sqn file will have 440868 – 441930.
Any ideas what might be causing this?
 
Thanks,
Brian




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