Question: Multifactor RNA-Seq analysis and interation terms
gravatar for Lance Parsons
14 days ago by
Lance Parsons110
United States
Lance Parsons110 wrote:

One of the labs I work with regularly uses Galaxy for their RNA-Seq analysis. They have been doing very simple analyses up to this point, using DESeq2. However, they are moving toward more complicated experimental designs that will include additional factors, some of which (genotype for example) will be interaction terms. I have a few questions:

  1. I know Marius van den Beek added group tags in 18.09, which seem like they are at least one way to use multiple factors along with collections. Is there any primer/tutorial on using these? It’s not quite clear to me just yet.
  2. Does anyone have any thoughts or suggestions as to how one could add interaction terms (e.g. condition:genotype) to the DESeq2 wrapper? Does this functionality exist in a different Galaxy tool?
ADD COMMENTlink modified 10 days ago by Jennifer Hillman Jackson25k • written 14 days ago by Lance Parsons110

Hello Lance Parsons!

It appears that your post has been cross-posted to another site: This is probably better answered on the galaxy-dev list. My guess is the wrapper will need an update.


ADD REPLYlink modified 9 days ago • written 9 days ago by Jennifer Hillman Jackson25k
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