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Status (27 28 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., including both merged and joined paired-end reads.

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

Demultiplexing and splitting

...

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 the joined 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

In /project/microbiome/data/seq/gtl_tests/iSeq100Pilot1_brew_30nov20/otu, I ran run_slurm_mkotu.pl, which I modified to also pick up the joined reads (in addition the merged reads). On I reran this with a modification to correctly and unique label (assign names to) otus in the table that is used as a database for otutable generation. . next upThese jobs should be complete later on .