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In /project/microbiome/data/seq/cu_24feb21novaseq4/otu, I ran run_slurm_mkotu.pl, which I modified to also pick up the joined reads (in addition the merged reads). I reran this on to address an error in how we using vsearch, whereby unique sequences were being incorrectly merged in the otutable because they did not have unique names (runs should be done late on .
Make coligo table
In /project/microbiome/data/seq/psomagen_6mar20/coligoISD, /project/microbiome/data/seq/psomagen_26may20/coligoISD, and /project/microbiome/data/seq/psomagen_29jan21novaseq1c/coligoISD, there are 16S and ITS directories for all projects. These contain a file named coligoISDtable.txt with counts of the coligos and the ISD found in the trimmed forward reads, per sample. I did not do the fanciness I did for the otutable generation with project renaming (see above). The file run_slurm_mkcoligoISDtable.pl has the code that passes over all of the projects and uses vsearch for making the table.