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To access this count table:
Go to the W:\training\rnaseq\runs\run3_RNAseq\results folder that contains the results from running the nfcore/rnaseq pipeline. The output folders from task 3 look like this:
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The count table can be found in the star_salmon folder. A list of files and folders in the star_salmon folder will look like this:
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a. First create a new folder in H:\workshop\RNAseq . Call it something suitable, such as ‘DE_analysis_workshop’
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e. Open RStudio and create a new R script (‘File’ → “New File” → “R script”). Now hit ‘File’ → ‘Save’ and save the script in the analysis workshop folder you created in step a. (NOT IN THE ‘data’ FOLDER). Give the script file a name (e.g. DESEq2.R)
The following analysis contains R code (in the grey text boxes) that you can copy and paste, then run, into the R script you just created.
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