Question: Visualizing CuffDiff Data
gravatar for nashedm
3.4 years ago by
United States
nashedm10 wrote:


I've run an RNAseq experiment to look for differentially expressed genes using CuffDiff. I've been using the Tuxedo protocol thus far and wanted to continue by using CummeRbund to visualize my results and create graphics for publication, but I noticed that CummeRbund is not included in Galaxy. Some other protocols also use tools such as edgeR and DESeq, which they cite as being found under "NGS: RNA analysis" in Galaxy, but I don't have seem to have this set of tools in Galaxy.

Are there other similar tools I can use to explore and visualize differential gene expression, novel splicing events, etc in Galaxy? Is there a way to add tools such as CummeRbund that I'm unaware of? I can always use the desktop version of CummeRbund with RStudio, but I'd rather avoid this option if possible as I do not have any coding experience. An online interface would be preferable. 


ADD COMMENTlink modified 3.4 years ago by Jennifer Hillman Jackson25k • written 3.4 years ago by nashedm10
gravatar for Jennifer Hillman Jackson
3.4 years ago by
United States
Jennifer Hillman Jackson25k wrote:


The RNA-seq tools on the public Main Galaxy instance can be found in the tool group "NGS: RNA-seq". Those not on Main may be in the Tool Shed, for use in a local or cloud Galaxy build (and sometimes other public Galaxy servers). These mentioned are. Most any 3rd party tool not present there could be wrapped for use in Galaxy, if you have programming resource available (yourself or other support/collaborators).

More about Galaxy server choices is included in this wiki: BigPicture/Choices

Hopefully this helps to explain how to use tools, on Main and on other servers, Jen. Galaxy team

ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by Jennifer Hillman Jackson25k
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