> I tried replying to the galaxy userlist but it said its for authorized users only, and i asked for permission but no response yet.
You can manage your subscription to galaxy-user here:
> I just had one quick question, the output files from of CDS diff, promoters diff and splicing diff from cuffdiff only report have sqrt(JS), teststat, and p value stats?
Correct. You can find full details of Cuffdiff's outputs in the manual:
These type of questions--questions about to use Galaxy--are best directed to
the galaxy-user list, so I've moved it there.
> I saw this thread, though it is older I just want to make sure I did my
> analysis after the update.
> You mention having to repeatedly merge cufflinks output for cuffcompare to
> generate the combined transcripts. I was able to add them all in the
> cuffcompare section with the "add new Additional GTF input file". also my
> command is:
> cuffcompare -o cc_output -r
> /galaxy/main_database/files/002/048/dataset_2048606.dat -R -s
> /galaxy/data/hg19/sam_index/hg19.fa ./input1 ./input2 ./input3 ./input4
> ./input5 ./input6 ./input7 ./input8 ./input9 ./input10
This is correct: Galaxy now supports an arbitrary number of input files to
cuffcompare, making repeated merging unnecessary.
> Also I was reading on seqanswers that cuffdiff didn't work with biological
> http://seqanswers.com/forums/archive/index.php/t-7905.html, but when I did
> my galaxy analysis it had the "perform replicate analysis" available and was
> wondering if you had an updated version or did something else. I am
> analyzing a control and diseased group, with 5 biological samples in each
> group. Cuffdiff should work fine on this right? I got FPKM as output.
> Also do you know what statistical methods cuffdiff is using for analysis?
Cuffdiff claims to support biological replicates, and, as you found, Galaxy
provides the infrastructure to specify replicates to Cuffdiff. I do not know
the statistical methods used for analysis, but this would be a good question
to ask either on seqanswers or on the new tophat-cufflinks mailing list:
> Lastly, in cuffdiff, the CDS, promoters and splicing analyses didn't seem
> to work (datasets 190,191,192). any ideas?
This is because the p_id attribute is not being attached to the
combined_transcripts dataset produced by Cuffcompare. This problem is due to
your reference file being incorrect -- it should be dataset 81, your
Please send questions such as these to the galaxy-user mailing list (which
I've cc'd). You can find the 'Extract Genomic DNA' tool under the 'Fetch
Sequences' menu. You may also want to use tool search ('Options -> Show Tool
On Wed, Mar 2, 2011 at 2:31 PM, <dinesh(a)gwu.edu> wrote:
> Hi Jeremy,
> You have asked to extract only the exons using the 'Extract Features'
> tool but all I see here in my developer version under 'Extract Features' is
> 'Gene BED To Exon/Intron/Codon BED expander'. But the cufflinks files is a
> gtf file... I have tried to use the above tool but it returns an empty file.
> Do I need to convert my gtf to bed and then extract the exons and then use
> the 'Extract Genomic DNA' tool?
> Thank You
> Dinesh Cyanam
> George Washington University
Sorry Jeremy, I'm being a bit dense here - where exactly are these tools in
> the tool list - I can't find them...
Both tools are located within the 'Operate on Genomic Intervals' menu. Also,
remember that tool search (Options -> Show Tool Search) is useful for
finding a tool.
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!
Ying Zhang, M.D., Ph.D.
Department of Genetics,
Yale University School of Medicine
300 Cedar Street,S320
New Haven, CT 06519
Are you still have problems? Updating to the most current distribution
dated Feb 18th would be advised, as a starting point:
hg pull -u -r ca0c4ad2bb39
Please give this a go and let us know if there continue to be issues
with using the save icon on your local instance.
On 2/17/11 6:52 AM, vasu punj wrote:
> I had problem in the past saving sam file from Galaxy's floppy sign and
> at that time Jen mentioned there was a bug which was fixed. After a
> month or so I cannot save the file. Any one has any suggestion please. I
> am running Galaxy on local server.