Question: sam to counts in toolbox
gravatar for jungminh
4.3 years ago by
United States
jungminh0 wrote:

I am trying to run DEseq with my rna seq data. 

I am following the tutorial ""

but I don't see "NGS: RNA Analysis" menu in my toolbox. my toolbox has a tag "beta"  but not in the tutorial. 

"Sam to counts" and "DeSeq" under NGS:RNA Analysis are what I need to use. 

Could you explain how I can get NGS:RNA Analysis? 

rna-seq • 1.1k views
ADD COMMENTlink modified 4.3 years ago by Jennifer Hillman Jackson25k • written 4.3 years ago by jungminh0
gravatar for Jennifer Hillman Jackson
4.3 years ago by
United States
Jennifer Hillman Jackson25k wrote:


All tools are not on the public Main Galaxy instance (, nor are they installed by default on local/cloud Galaxy instances (, Search in the Main ToolShed ( for specific tools needed and install on a local/cloud, and if they are not yet published or available there for some reason, you can contact the tutorial authors about the recommended tool access path (alternate public server or ToolShed repositories).

Hopefully one of these options works out for you! Jen, Galaxy team

ADD COMMENTlink written 4.3 years ago by Jennifer Hillman Jackson25k
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