Hello Olivier,

When deleting data, it takes the server a short amount of time to refresh. It may take a bit longer right now since many people are performing this action at the same time.


For the RNA-seq analysis question, reference annotation GTF files are used by the Cuff* programs. (These are different than the result GTF files produced by the programs). For reference annotation GTF files, there are many sources, including Ensembl and UCSC. Here are links to a tutorial and an FAQ that can help with your usage question.
http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise
http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq

But, there are many small details to running the tools to get the optimal results. These types of questions concerning functionality are best directed to the tool authors at tophat.cuffli...@gmail.com

Take care,

Jen
Galaxy team

On 10/25/11 11:24 PM, GANDRILLON OLIVIER wrote:
Hello Jennifer


Le 26/10/11 02:15, « Jennifer Jackson »<j...@bx.psu.edu>  a écrit :

Hello Olivier,

Are you using a reference gene annotation GTF file?

Well if I do , I do not know :-)

What I used is first TopHat and then Cufflink. At what stage shall I use
such a GTF file?
And additionnaly: where shall I find such a GTF file?

As I understand it: there are tow sources for a GTF file:
1. The output from cufflinks generates one (but there is no gene names in
it..)
2. I could get one from Ensembl?

Shall I then use Cuffcompare on the cufflink output?

Best

Olivier

PS: I am now stuck with the galaxy websute that state that I am over my
disk quota. I have deleted a couple of files but this does not seems to
help...



--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support
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