Dear David:

I followed your advices and downloaded reference sequence from Emsemble, then I
uploaded this file into galaxy, and then I run the cufflinks using the file as a
reference annotation, however I got error when I am running, the following the
error message gave to me:

An error occurred running this job: cufflinks v0.9.3
cufflinks -I 300000 -F 0.050000 -j 0.050000 -p 8 -Q 0 -G
/galaxy/main_database/files/002/122/dataset_2122219.dat -r
/galaxy/data/hg19/sam_index/hg19.fa
Error running cufflinks. [11:47:14] Loading reference and sequence.
GFF warning: mergi

Do you have any idea of what is going wrong here?

Best

Ying

Quoting David Matthews <D.A.Matthews@bristol.ac.uk>:

> Hi,
>
> Yeah, thats a good idea too!! I did not know about that tool, shows what I know (!) - thanks for the info!
>
> Cheers
> David
>
>
>
> On 1 Mar 2011, at 04:51, Jeremy Goecks wrote:
>
>> Ying, you could also try using the tools 'Fetch closest non-overlapping feature' and 'Intersect' to find genes nearby transcripts/genes/TSSes of interest; for both tools, you'll want a reference annotation, either from UCSC or Ensembl.
>>
>> Best,
>> J.
>>
>> On Feb 28, 2011, at 6:10 PM, David Matthews wrote:
>>
>>> Hi,
>>>
>>> You need to supply a gene annotation file with cufflink to easily get the gene-id information. Without it, cufflinks simply tries its best to figure out what genes are present. The ensemble gtf file is quite a comprehensive one - there is a link to it on the cufflinks manual page.
>>>
>>> Good luck!
>>> David
>>>
>>>
>>>
>>> On 28 Feb 2011, at 21:33, Ying Zhang wrote:
>>>
>>>> Dear Everyone:
>>>>
>>>> I have got one output file after I run Cufflink which contain gene expression
>>>> information. However, I found out for each gene_ID, it has the format like,
>>>> CUFF.1151175, do you have idea of how to find out the offical gene ID
>>>> correspond to this CUFF ID? Thank you very much!
>>>>
>>>> Best
>>>>
>>>> Ying Zhang, M.D., Ph.D.
>>>> Postdoctoral Associate
>>>> Department of Genetics,
>>>> Yale University School of Medicine
>>>> 300 Cedar Street,S320
>>>> New Haven, CT 06519
>>>> Tel: (203)737-2616
>>>> Fax: (203)737-2286
>>>> _______________________________________________
>>>> The Galaxy User list should be used for the discussion
>>>> of Galaxy analysis and other features on the public
>>>> server at usegalaxy.org. For discussion of local Galaxy
>>>> instances and the Galaxy source code, please use the
>>>> Galaxy Development list:
>>>>
>>>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>>>>
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>>>>
>>>> http://lists.bx.psu.edu/
>>>
>>>
>>> _______________________________________________
>>> The Galaxy User list should be used for the discussion
>>> of Galaxy analysis and other features on the public
>>> server at usegalaxy.org. For discussion of local Galaxy
>>> instances and the Galaxy source code, please use the
>>> Galaxy Development list:
>>>
>>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>>>
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>>>
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>>
>

Ying Zhang, M.D., Ph.D.
Postdoctoral Associate
Department of Genetics,
Yale University School of Medicine
300 Cedar Street,S320
New Haven, CT 06519
Tel: (203)737-2616
Fax: (203)737-2286
_______________________________________________
The Galaxy User list should be used for the discussion
of Galaxy analysis and other features on the public
server at usegalaxy.org. For discussion of local Galaxy
instances and the Galaxy source code, please use the
Galaxy Development list:

http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other
Galaxy lists, please use the interface at:

http://lists.bx.psu.edu/