Consensus Transcriptome

[aboddy]

Hello,

First time posting here I am attempting to assemble a de novo mammalian transcriptome from Illumina GAII 76bp paired end library. I am looking for suggestions for the best tool to make an consensus (non-redundant) transcriptome from the assembled contigs. That is, I have already assembled the reads into contigs (using Trinity) and now looking for the best tool to take me through the next step, making a consensus transcriptome that is non-redundant that can be used for down stream analyses (multiple sequence aligners, i.e. MUSCLE). I have read up on CAP3, but does anyone have an comments on this, will it produce a non-redundant output?

Thanks in advance.

[NRP]

I see there hasn't been much of a response here... Did you ever come up with a solution to this problem? I am currently facing the same issue: I just finished some assemblies in Trinity and now I want to try to merge related sequences to get a less redundant 'transcriptome'.

It seems like using CAP3 next might be a good choice. I was thinking of doing the same based on what I read in this paper:
Cahais V, Gayral P, Tsagkogeorga G, Melo-Ferreira J, Ballenghien M, et al. (2012) Reference-free transcriptome assembly in non-model animals from next-generation sequencing data. Molecular Ecology Resources.

I'd love to hear some comments on this approach from anyone who has done it before though.

[mmcgo002]

Hi.
I also posted here, please see the comments, but I did use CAP3 after my Trinity assembly.

http://www.biostars.org/post/show/43037/de-novo-transcriptome-and-comparative-genomics/

[Joshua_HIT]

Hi
I have tried to use GMAP as the downstream software for Trinity's output. After that I got sam documents. My classmates said the sam documents can be treated by any MSA software, but I don't know too much detail.