Hi Yona Kim,
On 4/18/13 9:54 PM, Yona Kim wrote:
Thank you very much for your help for my analysis.
I'm still stuck on getting the final data from Cuffdiff analysis.
As you have mentioned, I've obtained the correct GTF file (mm9 gene
annotation), and also made sure that the reference genome and GTF file
are an exact match - they both are mm9.
Are you using the iGenomes version of the GTF file? With the attributes
Cuffdiff requires for generating all of the additional statistics? It
appears that this is the case, but I just wanted to double check. If not
using it, you can find a copy to load and use on the public server (if
this is where you are working) in Shared Data -> Data Libraries ->
iGenomes. Otherwise, it can be found at the Cufflinks web site.
These are the two attributes that are important to have, when available:
The results you are getting indicate the data coverage is sparse, which
aligns with your thoughts about this mapping not being as successful as
When I view the output of transcript differential expression testing
(one of the outputs of cuffdiff) in excel, the names of the genes seem
to be properly annotated according to their location on chromosome, but
I have no values recorded for any of the calculations (I'm attaching
this file just in case you want to take a look at it).
NOTEST and LOWDATA are explained here with advice about parameter tuning:
follow links to Cufflinks FAQ to find:
Do you think that the problem might have been originated from fastq
And also I was wondering about the reduce in the size of the files.
Comparing with one of my other analysis in galaxy, I realized that the
size of the file was significantly reduced from 6.1GB (fastq groomer) to
1006.9KB (Tophat accepted hits), whereas in my other analysis, the size
was reduced from 5.9GB (fastq groomer) only to 1.6 GB(Tophat accepted
Do you think there might have been an error occurred when Tophat was
running on the groomed data, and thus, providing an erroneous data to
Cufflinks, and eventually to Cuffdiff?
This could be the source of the problem. Making sure that the data was
groomed correctly would be a good place the start. The comments from the
first run will note the detected input type (but there can be some
overlap), so also use the tool "FastQC" to help determine the proper
settings for "FASTQ Groomer". And if necessary, re-run from this step to
see if that improves the mapping.
See the second bullet under "FASTQ"
If your query data is short (less than around 40 bases), then tuning
Tophat could also improve mapping, see the tool's web page for advice
regarding mapping shorter sequences. Then test out a few different
parameter options to see what produces the best results for your
particular datasets/samples. There is a balance between being too
sensitive and too stringent - and this is a judgement call in most cases.
Trimming the reads may help if quality is an issue ("FastQC" will also
give information about this). The RNA-seq example tutorial has an
example of how to do basic QC:
Hopefully this helps to give some new options to test out that improve
Thank you very very much for your time and help
Department of Genetics
On Mon, Apr 8, 2013 at 4:54 PM, Jennifer Jackson <j...@bx.psu.edu
Yes, the GTF file is most likely the problem due to it lacking
certain attributes that Cuffdiff requires to perform these
calculations. You will also want to double check that the reference
genome and GTF file (where you source it next) are an exact match -
both the genome build and the identifier format. If either are not a
match, you will not get the expected or full results that Cuffdiff
This wiki has some help;
See "Tools on the Main server: Example → RNA-seq analysis tools."
The links to the Cufflinks web site explains the attributes that
Cuffdiff is looking for, links to the iGenomes datasets available
(best to use if your genome is represented), and a pointer to the
tool's user group. Two iGenomes GTF files are also already available
in Galaxy (hg19, mm9) in "Shared Data -> Data Libraries ->
iGenomes". The link to our tutorial and FAQ has help about how the
GTF files are used along with troubleshooting advice.
On 4/3/13 8:28 AM, Yona Kim wrote:
Dear galaxy users
Hello. I have a quick question about Cuffdiff analysis.
I have obtained two SRA files and converted them to fastq files
which were uploaded to Galaxy via FTP server. My analysis was
followed by Fastq groomer, Tophat, Cufflinks, Cuffcompare, and
eventually Cuffdiff. (Gene annotation was also downloaded from
UCSC table browser in GTF format) I've downloaded gene
differential expression testing, one of the output files of
Cuffdiff, and viewed it in excel sheet. However, I have only zeros
recorded for value_1, value_2, log2, test_stat and only ones
recorded for p_value and q_value.
Is it likely that I might have obtained wrong gene annotation file
and caused this problem?
Department of Genetics
Rutgers University - New Brunswick Campus
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