Hello Irene,

Yes, if using CuffDiff with a reference GTF file, all inputs must in present. One way to create this GTF is using CuffCompare.

Our example protocol is to run CuffMerge (which runs CuffCompare as part of the process) with all inputs prior to running CuffDiff. The updated RNA-seq tutorial covers the details:
http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise

The Cufflinks website has some sample protocols where CuffCompare is used alone (without proceeding to CuffDiff).
http://cufflinks.cbcb.umd.edu/tutorial.html#discovery
I know that we have pointed there before, but it really is the best resource (what the content on Galaxy is based on), along with the primary paper and tophat.cuffli...@gmail.com support.

Best,

Jen
Galaxy team

On 8/10/12 12:44 AM, i b wrote:
Dear all,
given 3 samples, 1 control and 2 treated replicates when I do
cuffcompare to produce the gtf input for cuffdiff, do I have to run it
with or without the cufflink control?
E.g. Cuffcompare with only my 2 treated replicates?--------------use
this gtf to run cuffdiff
        Cuffcompare 1 contro and 2 treated replicates?--------------use
this gtf to run cuffdff

Thanks a lot
ib
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  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/


--
Jennifer Jackson
http://galaxyproject.org
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  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/

Reply via email to