Question: DEseq2 collapseReplicates (Technical Replicates) function in Galaxy
gravatar for iraplee
14 months ago by
iraplee0 wrote:

Hi, I'm looking to see if there is a way to collapse RNA-Seq technical replicates into one on Galaxy. I believe DESeq2 has the ability to do it through collapseReplicates. However, I don't see any sort of option to do so through Galaxy's GUI DESeq2. Are there other ways of doing this?

My current pipeline for RNA-Seq analysis --> fastqsanger file --> HISAT2 --> featureCounts --> DESeq2

rna-seq galaxy • 651 views
ADD COMMENTlink modified 14 months ago by Devon Ryan1.9k • written 14 months ago by iraplee0
gravatar for Devon Ryan
14 months ago by
Devon Ryan1.9k
Devon Ryan1.9k wrote:
  1. Merge the technical replicates on their shared ID column
  2. Sum the two columns of counts.
  3. Select only the first ID column and the sum column

You can use that as the input into DESeq2. In RNAseq, technical replicates are collapsed by simply adding their per-gene counts together.

ADD COMMENTlink written 14 months ago by Devon Ryan1.9k
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