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Status (27 February 2021)

  • Alex Buerkle has processed the data to the point before OTU table generation and will do that next. I coded the many new steps from Bioinformatics v3.0 for parallelism across loci and projects.

These are the informatics for the Bioinformatics iSeq100 Pilot1 library prep.

...

Within each of these directories are files for the trimmed, merged, and filtered reads. In each of these directories, there are subfolders trimmed/, joined/, and unmerged/ (the last one is used as a working directory, should be empty; unmerged reads are filtered and joined and put in joined/ if they can be joined; this directory can be empty, if all unmerged reads were coligos for example). For example, see contents of /project/microbiome/data/seq/gtl_tests/iSeq100Pilot1_brew_30nov20/tfmergedreads/16S/brew_20/

Make OTU table

... next upIn /project/microbiome/data/seq/gtl_tests/iSeq100Pilot1_brew_30nov20/otu, I ran run_slurm_mkotu.pl (not yet modified to incorporate potential joined reads, of which there were none in this project).