Hello Wei,
The results do sound strange. The best advice to start with is to make
sure that you are up-to-date with both Galaxy and the RNA-seq tools and
using the best possible inputs.
1 . Make sure that you are running the latest distribution
http://wiki.galaxyproject.org/DevNewsBriefs
2. Update to use the current version of CuffDiff
http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies
3. Use the iGenomes GTF annotation to make full use of the
functionality in Cuffdiff
http://cufflinks.cbcb.umd.edu/igenomes.html
A good test to see if your set-up is correct would be to run the RNA-seq
tutorial locally as a test case.
http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise
The reverse can also be done, if you have a problem locally, try running
it as a small test (that still demonstrates the issue) on the Public
Main server and see if the results can be duplicated. This can help
determine if problem is with data inputs/settings or a problem with tool
set-up/installation. It can also be a way to share your data with us if
you need feedback.
But, hopefully after updating the issue clears up!
Jen
Galaxy team
On 11/29/12 11:51 AM, Wei Liao wrote:
Hi, Galaxy user.
I ran into a problem when using Cuffdiff 1.2.1 in Galaxy local
instance to check differential expressed genes in my samples.
I have 3 normals and 6 cancers samples, I did the following:
- After tophat for each samples, run cufflink with refseq annotation
which has 25266 genes and 43091 transcripts
- cuffmerge all cufflink outputs contains 58112 lines
- run cuffdiff with 3 normals as triplicate and compare to each cancer
sample.
Suprisingly, I fould out that the tanscripts tracking file, gene
tracking, CDS tracking only has 2000 genes and 4000 transcripts. So
the cufflink only compare 2000 genes and 4000 transcripts between
samples.
The question I want to ask here is that *why are the rest of the genes
and transcripts not being tested and included in the tracking files?*
Do you know what cause this kind of problem?
Thanks,
Wei
--
Wei Liao
Research Scientist,
Brentwood Biomedical Research Institute
16111 Plummer St.
Bldg 7, Rm D-122
North Hills, CA 91343
818-891-7711 ext 7645
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