Question: Analyzing CuffDiff output
gravatar for adam2689
3.2 years ago by
United States
adam26890 wrote:

Hi All,


I'm a grad student at the University of Alabama at Birmingham using galaxy for the first time.  I've successfully gone through the TOPHAT, CUFFLINKS, CUFFDIFF pipeline and have generated the transcript differential testing file.  Is there a way to use that file as an input for gene ontology analysis, or a better tool to look at potential pathways?  I've watched tutorials where people use CUMMERBUND, but that looks like it is mostly useful for visualizing changes in levels of known genes.




galaxy • 1.3k views
ADD COMMENTlink modified 3.2 years ago by Jennifer Hillman Jackson25k • written 3.2 years ago by adam26890
gravatar for Jennifer Hillman Jackson
3.2 years ago by
United States
Jennifer Hillman Jackson25k wrote:


The most commonly used tool for this sort of analysis that I know of is LEfSe. This is tools is available in the Tool Shed for use in a local or cloud Galaxy. A search by "GO" in the Tool Shed will bring up other options to review. See the 3rd party documentation for each tool to review usage details. Most Galaxy wrappers incorporate at least the major parameters for common usage. 

Also, if you used a reference GTF dataset with the analysis, then the attribute gene_name assigned to the output can be used with several tools in the group "Phenotype Association". If you need to map gene names or symbols but you have the wrong ones in your output (to match the target tool), the "xref" table associated with several genomes from UCSC can be helpful in converting terms. Obtain this table from the UCSC Table Browser. The idea would be to join the list of terms you have with that table to link in another source's terms, then use those new terms as input as a link to GO. This is a bit more tedious to do, but is an option.

Hopefully this helps, Jen, Galaxy team

ADD COMMENTlink written 3.2 years ago by Jennifer Hillman Jackson25k
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