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Status (9 March 2021)
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| Table of Contents |
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Demultiplexing and splitting
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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).This is where I am as of (steps above have been launched). Alex Buerkle will continue from here . The steps below have not yet been started; they contain notes for what I will do.
Make OTU table
In /project/microbiome/data/seq/cu_24feb21novaseq4/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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This is where I am as of (the otu table generation has been launched).