Re: [Transdecoder-users] TransDecoder help

[Elasady, S. <sr...@st...>]

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
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