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ALF1_16S_Demux.csv is used to map MIDS to sample names and projects.
Stopped here on 9-20-22
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Splitting to fastq for individuals
The info lines for each read in parsed_ALF16S_R1_*.fastq and parsed_ALF16S_R2_*.fastq have the locus, the forward mid, the reverse mid, and the sample name. These can be used with the demux key to separate reads into loci, projects, and samples, in the folder sample_fastq/. The reads are in separate files for each sequenced sample, including replicates. The unique combination of forward and reverse MIDs (for a locus) is part of the filename and allows replicates to be distinguished and subsequently merged.
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In /project/gtl/data/raw/ALF1/16S/coligoISD and /project/gtl/data/raw/ALF1/16S/otu 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. The file run_slurm_mkcoligoISDtable.pl has the code that passes over all of the projects and uses vsearch for making the table.
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