Hi Davide, Yes, if the iGenomes annotation data collection includes a reference GTF dataset for your genome, that would be the best choice, as it would include all of the attributes that the RNA-seq tools (Cufflinks, CuffDiff, etc) require for full functionality. The hg19 and mm9 GTF files are on the public Main Galaxy instance Shared Library "iGenomes". The complete set is located at the Cufflinks web site here: http://cufflinks.cbcb.umd.edu/igenomes.html The RNA-seq tutorial also uses the iGenomes dataset - so perhaps you are referring to the prior version, or possibly the FAQ that provides help with converting formats (may be necessary if an iGenomes dataset is not available for a particular target genome)? In any case, latest tutorial is located here and represents the most current 'best practice' guidelines we have for this tool set: http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise Hopefully this helps, Jen Galaxy team On 1/29/13 8:28 AM, Davide Degli Esposti wrote:

Dear all,

I am trying to get an exhaustive reference annotation for RNA-Seq analysis. I was thinking that the patched GTF annotation files for cufflinks Jeremy indicates in RNA-Seq step by step tutorial should be fine for me, but I am not able to find on the Shared data > Data libraries. Have they been replaced by iGenomes annotations?

I thank you for your help

Best regards

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