Hello Miro,

for these kind of general questions I would recommend you to ask in the
bioinformatics forum at http://www.biostars.org/ as it is somewhat
unrelated to Galaxy.

Nevertheless some of the tools you mentioned are installed and available on
the main instance (usegalaxy.org) and some you can install on your own
Galaxy via the Toolshed (http://toolshed.g2.bx.psu.edu/).

best

Martin, Galaxy Team


On Mon, Nov 25, 2013 at 4:16 PM, miroslav.sotak <miroslav.so...@upjs.sk>wrote:

>
> To whom it may concern
>
> I would like to kindly ask you if you do have any experience in de-novo
> transcriptomic analysis (no reference genome available) who might give us
> some advice.
> Our main question is how to create the best set of cDNA contigs, on which
> we can map our RNAseq reads for the analysis of differential expression.
> Currently 4 larger sets of of RNAseq reads are available from different
> genotypes as well as draft genome assembly for one of the genotypes. We
> worry about the SNPs in different genotypes affecting the assembly, if we
> combine all the RNAseq datasets and using assemblers such as Trinity,
> Oases, Velvet. Might it be better to use the draft genomic assembly to
> obtain cDNA contigs using Tophat/cufflinks via all available RNAseq data or
> only using the RNAseq data from the same genotype as the genome draft?
>
> Thank you in advance
> Best wishes
> Miro Sotak
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