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Overview

Table of Contents
stylenone

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Code Block
cp -r /work/training/metagenomics/public_data/Illumina/results $HOME/meta_workshop/illumina
mkdir -p $HOME/meta_workshop/illumina/data
cp -r /work/training/metagenomics/public_data/Illumina/data/metadata.tsv $HOME/meta_workshop/illumina/data

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In session 7 we’re going to do some downstream analysis of the nfcore/sarek variant calling workflow that was completed in sessions 2 and 3 of these workshops. We realise not everyone attended these (or didn’t successfully complete the sarek workflows), so you can download the results of successful runs by running the following command in PuTTY:

Code Block
cdmkdir $HOME/workshop/workshops
mkdir sarek
cp -r /work/training/sarek/runs/ $HOME/workshopsworkshop/sarek

While these datasets are copying we can move to the next section (leave PuTTY running).

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Create a new script by ‘File’ → “New File” → “R script”. Now hit ‘File’ → ‘Save’ and save the script in H:/meta_workshop/R_analysis (i.e. the directory we just created). Give the script a name. Call it “R_metagenomics”.

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