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The analysis also requires the metadata.tsv file we created at the start of last workshop. Check to see if this file is in Z:\meta_workshop\illumina\data
If you don’t have can’t see the ASV_table.tsv or metadata.tsv files (your Nextflow job may have failed, for example), open PuTTY and run the following to copy these from a successful nfcore/ampliseq run to your HPC home directory:
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cp -r /work/training/metagenomics/public_data/Illumina/results $HOME/meta_workshop/illumina cp -r /work/training/metagenomics/public_data/Illumina/data/metadata.tsv $HOME/meta_workshop/illumina/data |
We’ll need to Open PuTTY and also create a working directory to store our R scripts and the results of today’s analysis.
In PuTTY run the following to create today’s workshop folder:
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mkdir $HOME/home/whatmorp/meta_workshop/R_analysis
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