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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/
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In /project/microbiome/data/seq/gtl_tests/iSeq100Pilot1_brew_30nov20/otu, I ran run_slurm_mkotu.pl (not yet , which I modified to incorporate potential also pick up the joined reads , of which there were none in this project(in addition the merged reads).