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.sotak@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 ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
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