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Gregg Randolph

Gregg Randolph

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Status (28 April 02 May 2022)

  • Data arrived by sftp on 28 April 2022. Everything below is a draft modified from Bioinformatics for Novaseq run 4 ). I will begin processing tomorrow, 4-29Data processing finished 5-12-22. Most of the text should remain the same. Current figures are irrelevant placeholders.

Table of Contents

Demultiplexing and splitting

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splitFastq.pl and splitFastq_manyInputfiles.pl will need tweaking in the future, whenever sample names and the format of the key for demultiplexing and metadata changes. The number of columns has differed among some of early sequence lanes, which necessitated changes to this parsing script.

Below This Point is yet to be done

Calculate summary statistics on reads

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In /project/microbiome/data_queue/seq/psomagen_6mar20NS5/coligoISD, /project/microbiome/data/seq/psomagen_26may20NS5/coligoISD, and /project/microbiome/data/seq/psomagen_29jan21novaseq1cNS5/coligoISD, 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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5-2-2022 Alex Buerkle transferred all of this to /project/microbiome/data/seq/cu_29april22novaseq5