RNA-Seq Differential Expression Analysis

Hello all,

I have paired/matched RNA-Seq data (eg. patients with 2 timepoints, one before and one after their treatment) and I would like to perform a pairwise analysis, using DESeq2, EdgeR or whichever tool is more appropriate. Your help would be much appreciated, especially the steps after getting the htseq_count files. Thanks a lot in advance

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Hi @gdivolis

Please see the Transcriptomics GTN tutorials. Most include a workflow that you can either use directly (if appropriate) or use as a baseline template when customizing your own. Or you can run the analysis directly without a workflow (sometimes better, especially if you are experimenting with parameters). You can always extract a workflow from the history once you have a functional process defined (for reuse yourself or to document/share your methods with others).

If you are new to Galaxy, you might want to first get oriented with a few Intro tutorials.

There is also much prior Q&A about DE analysis and related best practices/troubleshooting tips at this forum. Try searches using tool names as keywords. I added some tags to your post that will also find those discussions. For latest news (usually include learning resource updates), see: Topics tagged news

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