[maker-devel] tbl2asn errors

[Brian Hall]

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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