Multifactor RNA-Seq Analysis and interaction terms

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Multifactor RNA-Seq Analysis and interaction terms

Lance Parsons

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?

Thanks in advance.

-- 
Lance Parsons - Scientific Programmer
Carl C. Icahn Laboratory - Room 136
Lewis-Sigler Institute for Integrative Genomics
Princeton University

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