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Status (02 May 2022)
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| Table of Contents |
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Demultiplexing and splitting
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Statistics on the initial number reads, the number of reads that merged, and the number of reads that remain after filtering are in filtermergestats.csv in each project folder. Please note that this will not include the number of reads that failed to merge, but we were able to join. This category is likely to include ITS sequences for which the amplicon was large enough that our 2x250bp reads could not span the whole length. The greater number removed in ITS (orange) in the plot below is consistent with this idea. For the full lane these summaries were concatenated in tfmergedreads/ with
Below This Point is yet to be done
cat */*/filtermergestats.csv > all_filtermergestats.csv
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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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Make OTU table
In /project/microbiome/data_queue/seq/NS5/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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