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 Have they been replaced by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
Davide-----------------------------------------------------------------------
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