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changes.mady.by.user Alex Buerkle

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changes.mady.by.user Alex Buerkle

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  • compressed all sample_fastq/ files with pigz: using sbatch /project/microbiome/data/seq/HMAX1/demultiplex/run_pigz.sh

  • moved fastq for all four blank samples (data are all in one file because names are collapsed; noted above) to a subfolder (/project/microbiome/data/seq/HMAX1/demultiplex/sample_fastq/blanks), to get them out of the way.

  • started denovo assembly in /gscratch/buerkle/data/HMAX1/denovo Completed first step for dDocent and am running cd-hit for 92% and 96% minimum match. Will also probably run 92/ 98.

To do:

  • Summarize the parse report files in /gscratch with some code to iterate over all the individual reports and get an overall count.

  • variant calling

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