Re: [Transdecoder-users] TransDecoder help

[Brian H. <bh...@br...>]

and the gtf or gff3 formats are described here:
http://www.ensembl.org/info/website/upload/gff.html
or
http://www.sequenceontology.org/resources/gff3.html

best,

~brian

On Wed, Oct 29, 2014 at 12:40 AM, Elasady, Summer <sr...@st...> wrote:

> Hi-
>
> I asked Brian to decipher the output, and here is what he told me:
>
> Hi Summer,
>
> I'm not sure it's described anywhere yet...
>
> There appears to be some redundant info in the header. The important parts
> are:
>
> >cds.comp1000092_c0_seq1|m.177654 type:internal len:250 (+)
> comp1000092_c0_seq1:1-747(+)
>
> which can be broken down as:
>
> protein accession: cds.comp1000092_c0_seq1|m.177654
>    so, orf m.177654 on trinity transcript comp1000092_c0_seq1
>
> type: internal indicates that the transcript can be translated from
> beginning to end of the trinity transcript sequence (no start codon or stop
> codon detected).  Alternatively, this might indicate complete (full ORF),
> 3prime partial (missing stop codon) or 5prime partial (missing start codon)
>
> The length of the orf is 250 amino acids
> and the translation is done from the range of 1-747 on the trinity
> transcript, in the '+' orientation.
>
>
> Sent from my iPhone
>
> > On Oct 28, 2014, at 5:38 PM, Rebekah Ruth Starks <
> rst...@em...> wrote:
> >
> > Good Afternoon,
> >
> > My name is Rebekah and I am a first year pH D student. This is my first
> time using transDecoder and I am having a difficult time understanding the
> output and what each column corresponds to. Is there a place on the website
> that describes the output better? Thank you or your time. Have a great day!
> >
> > Bekah
> >
> ------------------------------------------------------------------------------
> > _______________________________________________
> > Transdecoder-users mailing list
> > Tra...@li...
> > https://lists.sourceforge.net/lists/listinfo/transdecoder-users
>
>
> ------------------------------------------------------------------------------
> _______________________________________________
> Transdecoder-users mailing list
> Tra...@li...
> https://lists.sourceforge.net/lists/listinfo/transdecoder-users
>



-- 
--
Brian J. Haas
The Broad Institute
http://broad.mit.edu/~bhaas