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Status (3 March 2021)
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In a sequence library’s rawdata/ directory (e.g., /project/microbiome/data/seq/cu_24feb21novaseq4/rawdata) I made run_aggregate.sh, to run aggregate_usearch_fastx_info.pl with a slurm job. Summaries are written to summary_sample_fastq.csv.
Trim, merge and filter reads
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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.
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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
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