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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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To access this count table:
Go to theW:\training\2024\rnaseq\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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1b. Sample Table - metadata
In the same W:\training\2024\rnaseq\run3_RNAseq\results\star_salmon directory there will be a file called metadata.xlsx . Copy this file to your ‘data’ folder as well. This file will normally need to be manually created by you to match your sample IDs and treatment groups, but we created this file already for you to use. This samples table needs 3 columns called ‘sample_name’, containing the sample names seen in the count table (column names), ‘sample_ID’, which is the (less messy) names you want to call the samples in this analysis workflow, and ‘group’, which contains the treatment groups each sample belongs to. The contents of this file look like this:
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