Bioinformatics Forum

Pipeline for RNA-Seq

What is the workflow for RNA-Seq analysis and which tools are used?

Gilgi Friedlander
1 Answer

Hi Gilgi, 

This is the workflow and tools that are used in the RNA-Seq pipeline, with the current versions:

  1. Mapping - TopHat (V 2.0.10)
  2. Counting - HTseq-count (V 0.6.1p1)
  3. Differential Expression Analysis - DESeq2 (V 1.6.3)

More information on the pipeline can be found here:

https://incpmpm.atlassian.net/wiki/display/PUB/RNA-seq+on+Pipeline+Pilot

 

Nofar Chen

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