Dear Jennifer

Actually the problem was coming from a non usable Ensembl GTF file. I used
the workflow in
http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq
And remade the Cufflink analysis using the new GTF file as a reference
and, BINGO, it worked.

Thank's for your help

Best

Olivier


Le 28/10/11 20:19, « Jennifer Jackson » <j...@bx.psu.edu> a écrit :

>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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