[maker-devel] tbl2asn errors

[Shaun Jackman]

Hi, Scott, Carson. What's currently the best/easiest way to convert a MAKER
GFF to GenBank TBL format, and what's the state of your GAG tool, Scott?

Cheers,
Shaun

*http://sjackman.ca <http://sjackman.ca>*

On 17 April 2014 15:37, Geib, Scott <Scott.Geib at ars.usda.gov> wrote:

>  Just so not to be discouraged, current version has limited functionality
> and is pretty much un-documented (although will write a .tbl file).  Will
> email the list when first real release is complete and documented.
>
> Scott
>
>
>
>
>
>
>
> *From:* Carson Holt [mailto:carsonhh at gmail.com]
> *Sent:* Thursday, April 17, 2014 11:28 AM
> *To:* Geib, Scott; Mack, Brian; maker-devel at yandell-lab.org; Brian Hall (
> bhall7 at hawaii.edu)
>
> *Subject:* Re: [maker-devel] tbl2asn errors
>
>
>
> 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: "    " <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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