Playing around with R for #indoorevol

James took us through a tutorial in R today – see Dropbox folder for the .md, .html, and .rmd files to view/execute in R.

I had to install these additional packages to use his scripts:

install.packages(‘knitr’)
install.packages(‘xtable’)
install.packages(‘picante’)

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#indoorevol metanalyses – fungi

Getting down to meta-analysis for the indoorevol project. Running Closed Ref OTU picking on Amazon Cloud, with a new fungi parameter file I compiled. Command ran:

pick_closed_reference_otus.py -i /home/ubuntu/data/fungi/Fungal_long_seqs.fasta -o /home/ubuntu/data/fungi/uclust_closedref_97 -r /home/ubuntu/data/fungi/its_12_11_otus/rep_set/99_otus.fasta -t /home/ubuntu/data/fungi/its_12_11_otus/taxonomy/99_otu_taxonomy.txt --parallel -O 8 -p /home/ubuntu/data/fungi/qiime_parameters_fungi.txt