Overview
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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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mkdir $HOME/meta_workshop/R_analysis |
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Downloading the sarek results
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:
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mkdir $HOME/workshop/sarek
cp -r /work/training/sarek/runs/ $HOME/workshop/sarek
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While these datasets are copying we can move to the next section (leave PuTTY running).
Open RStudio and create a new R script
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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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