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
2. Update to use the current version of CuffDiff
3. Use the iGenomes GTF annotation to make full use of the
functionality in Cuffdiff
A good test to see if your set-up is correct would be to run the
RNA-seq tutorial locally as a test case.
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!
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
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?
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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