Pipeline to perform DESeq2 analysis from a matrix containing raw counts per gene per sample, in at least two conditions, with at least two replicates per condition.
Pipeline website: http://utap.wexac.weizmann.ac.il
Setting up a new analysis
The transcriptome pipelines run on the Wexac cluster. In order to run a new transcriptome analysis, your fastq files must be in your Collaboration folder on Wexac, in the correct structure (UTAP requirements & description) .
Before running the pipeline, prepare your counts matrix file and transfer it to the Collaboration folder.
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Choose your counts matrix file using 'Input folder' and click on run DESeq2 in order to identify differentially expressed genes with the DESeq2 package as described in the DESeq2 manual.
All of the samples from the counts matrix file will be parsed to the popup "choice box" .
Fill in you desired report folder name in the relevant field.
When choosing to run DESeq2 (with the 'DESeq2 run'), at least two categories must be created (by filling in the category names and dragging the relevant samples). Additional explanations can be found in 16.2.22 UTAP: Transcriptome from RNA-Seq, MARS-Seq or SCRB-Seq.
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LINK:
Transcriptome pipeline for Weizmann Institute users: http://utap.wexac.weizmann.ac.il
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