Complete GUI pipeline for Illumina RNA-seq data

[JDBELGIUM]

Hi everyone,
First of all I would like to thank you all for the great job this website (and members) do!

I have several illumina RNA-seq data that I would like to analyse on a mac computer using GUI softwares (and if possible friendly-user).

I tried RobiNA which is great but as I need to perform de novo seq analysis I'm not sure it would be the best way.

My question is...Following your own experience.. Could you tell us your "best complete pipeline" to perform illumina RNA-seq analysis using mainly free GUI software?

[rhinoceros]

Have a look at Galaxy. Though you'd probably still need to set it up yourself and that's not necessarily trivial..

[GenoMax]

Besides galaxy, If you are set on using a GUI (and have money to spend on commercial software) then look at CLC Genomics Workbench (http://www.clcbio.com/).

That said you should consider putting some time in to learning the command line tools which you have the option of using on your Mac. This would broaden your choice of tools significantly. Trinity (http://trinityrnaseq.sourceforge.net/) is a possible option for RNA-seq as is the Tuxedo pipeline (Nature Protocols: http://www.nature.com/nprot/journal/....2012.016.html) Additional R-packages for differential expression analysis (DESeq2: http://www.bioconductor.org/packages...ml/DESeq2.html).

[usad]

Hi JDBelgium

I reckon when you say de-novo you mean from sequence=>assembly=>DE genes?
We considered this for RobiNA but at the moment transcriptome assemblies are still quite "heavy".

Best Wishes,
b