[maker-devel] tbl2asn errors

[Barry Moore]

Cool, thanks Brian,

B

Barry Moore
-------------------------------------------------
Director, Research & Science
USTAR Center for Genetic Discovery
Dept. of Human Genetics
University of Utah
Salt Lake City, UT
T: (801) 858-9476
C: (801) 243-8819

On Oct 6, 2014, at 10:02 PM, Brian Hall <bhall7 at hawaii.edu<mailto:bhall7 at hawaii.edu>> wrote:

Hi Barry,

Try this one:

http://genomeannotation.github.io/GAG/

Sorry about that!

--Brian Hall


On 10/06/2014 05:53 PM, Barry Moore wrote:
Hi Scott,

Just FYI, github is giving me a 404 error on the link below.  Were others able to follow the link successfully?

B

Barry Moore
-------------------------------------------------
Director, Research & Science
USTAR Center for Genetic Discovery
Dept. of Human Genetics
University of Utah
Salt Lake City, UT
T: (801) 858-9476
C: (801) 243-8819

On Apr 17, 2014, at 2:59 PM, Geib, Scott <Scott.Geib at ARS.USDA.GOV<mailto:Scott.Geib at ARS.USDA.GOV>> wrote:

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