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Aim:
Process metagenomics data using metadata groups ( --metadata metadata.tsv )to enable the generation of alpha and beta diversity analyses
Interactive HPC session
Open a Terminal (Mac users) or PuTTy (Windows users) and paste the text below into the command prompt to start an Interactive Session:
| Code Block |
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qsub -I -S /bin/bash -l walltime=4:00:00 -l select=1:ncpus=4:mem=8gb |
It should take less than a minute for the interactive session.
Running nfcore/ampliseq with metadata information
Metadata is optional to run the ampliseq pipeline, but for performing downstream analysis such as barplots, diversity indices (alpha and beta diversities) or differential abundance testing, a metadata file is essential.
The public data we are using in the workshop does not have associated metadata information, so we will used an ‘artificially’ created metadata.tsv file that assigns the first 15 samples to a “control” group and the remaining samples to a group called “illumina” (technology used to created the amplicon data.
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Move to the /results/qiime2/diversity folder and evaluate the alpha diversity results, particularly, open the interactive “index.html” reports for each type of alpha diversity generated:
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Move to the /results/qiime2/diversity folder and evaluate the beta diversity results, particularly, open the interactive “index.html” reports for each type of beta diversity generated:
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