Re: [Transdecoder-users] Transcoder question

[<Ale...@cs...>]

And I do the reverse (conduct the DE analysis on the ORFs) but that's because my approach is the same whether the genes come from Trinity or from genome annotations (PASA) so... Erik it's up to you either way your blast2go graphs will look the same :-)


________________________________
From: Brian Haas [bh...@br...]
Sent: Tuesday, 9 September 2014 11:25 AM
To: Erik Lysøe
Cc: tra...@li...
Subject: Re: [Transdecoder-users] Transcoder question

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...<mailto: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