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ALF1_ITS_Demux.csv is used to map MIDS to sample names and projects.
Stopped here on 9-20-22
Splitting to fastq for individuals
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cat */*/filtermergestats.csv > all_filtermergestats.csv
I used commands.R in that folder to make a plot of numbers of reads per sample (horizontal axis) and the number reads that were removed because they did not merge, or did meet quality criteria and were filtered out (vertical axis). Purple is for 16S and orange is for ITS. It might be interesting to do that plot for each of the projects in the library (TODO), and possibly to have marginal histograms (or put quantiles on the plots).
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Make OTU table
In /project/gtl/data/raw/ALF1/ITS/rawdata/otu, I ran run_slurm_mkotu.pl, which I modified to also pick up the joined reads (in addition the merged reads).
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In /project/gtl/data/raw/ALF1/ITS/coligoISD and /project/gtl/data/raw/ALF1/ITS/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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