What version of Cufflinks is your Galaxy installation running? A recent version
(1.00 and 1.01) had a problem that was causing the splicing and promoter use
tests to have very few differentially regulated genes, according to
http://cufflinks.cbcb.umd.edu/.
-rory
On Jun 16, 2011, at 8:13 AM, Fe
Is there a reason why just using the command line tool isn't workable for you?
Personally, I'm happy when I can just do something quick like that.
Also you can simplify your command with sort filename | uniq.
-rory
On May 6, 2011, at 9:45 AM, Roman Valls wrote:
> Hey galaxy users,
>
> Thats a
For the ensembl annotation, you can download the gtf file from ensembl for your
organism here:
http://uswest.ensembl.org/info/data/ftp/index.html
To use this, you need to fix it because the chromosome names are not correct
(depending on your organism, it is not correct for mouse and rat at leas
I am not sure about cuffcompare, but cuffdiff doesn't generate any extra files
if you add more groups and replicates to the command line. It adds columns to
the output files but the number of files remains the same.
For a workflow for Martin for now, I would suggest doing this for making calls
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