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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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Initially Alex Buerkle / I stopped there. But after finding an error in how we were using vsearch for other libraries, on I ran otutable generation for this library too. See otu/ for code and Joshua Harrison will continue, since otutables will involve reads from multiple librariesoutput. These data were not processed to work with joined reads (as we’ve done with other libraries. Joshua Harrison : please let me know if you’d like me to redo the trim, merge, join, filter step over again, and then rerun the otutable generation.