Re: [Transdecoder-users] TransDecoder Output

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

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.

best,

~brian






On Fri, Mar 21, 2014 at 11:02 AM, Elasady, Summer <sr...@st...> wrote:

>  Hello-
>
>  I'm trying to decipher the output files from Transdecoder and cannot
> find any documentation on what exactly is in each column. Can you please
> point me to the where this info is located? For example, in the .cds file,
> I have the following headers:
>
>  >cds.comp1000092_c0_seq1|m.177654 comp1000092_c0_seq1|g.177654  ORF
> comp1000092_c0_seq1|g.177654 comp1000092_c0_seq1|m.177654 type:internal
> len:250 (+) comp1000092_c0_seq1:1-747(+)
>
>  What does it all mean?
>
>  Thank you,
>
>  Summer R. Elasady
> Baumann Lab - Bioinformatics Intern
> SR...@st...
>
>
>
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-- 
--
Brian J. Haas
The Broad Institute
http://broad.mit.edu/~bhaas