Re: [Transdecoder-users] Transcoder question

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

Hi Erik,

I find it useful to combine all ORF annotations to annotate a given
transcript (ie. the transcript inherits the annotations from all it's
candidate peptides).  Then, if a transcript is found to be interesting (ie.
DE analysis), I would dig in further to determine which ORF is most
relevant in that context.

best,

~brian



On Mon, Sep 8, 2014 at 7:21 AM, Erik Lysøe <eri...@bi...> wrote:

>  Dear developers
>
>
>
> About de novo transcriptome. I know blastx is very time consuming, and got
> a suggestion to first use CD-HIT EST (too reduce redundancy), then
> transdecoder to convert to peptides and then blastp against ref-seq protein
> database to speed up transcriptome annotation. So far so good, but I have
> some problems. How to you normally proceed after transdecoder, when many
> cDNA contigs has several ORFs? Then each cDNA contig could have several
> annotations. I usually import the blast xml to Blast2go, and would like to
> only use one (best hit) annotation per cDNA contig for further analysis of
> the transcriptome.
>
>
>
> Any suggestions?
>
>
>
> Cheers Erik
>
>
>
>
>
>
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-- 
--
Brian J. Haas
The Broad Institute
http://broad.mit.edu/~bhaas