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Gregg Randolph

Gregg Randolph

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Assign reads and

...

otus to samples:

Code Block
/project/microbiome/data_queue/seq/LowReadII/rawdata

salloc --account=microbiome -t 0-06:00

mkdir -p /gscratch/grandol1/LowReadII/rawdata

cd /gscratch/grandol1/LowReadII/rawdata

unpigz --to-stdout /project/microbiome/data_queue/seq/LowReadII/rawdata/Low-Read-II_S1_L001_R1_001.fastq | split -l 1000000 -d --suffix-length=3 --additional-suffix=.fastq - LowReadII_R1_ ;unpigz --to-stdout /project/microbiome/data_queue/seq/LowReadII/rawdata/Low-Read-II_S1_L001_R2_001.fastq | split -l 1000000 -d --suffix-length=3 --additional-suffix=.fastq - LowReadII_R2_

//project/microbiome/data_queue/seq/LowReadII/rawdata/run_parse_count_onSplitInput.pl

cd /project/microbiome/data_queue/seq/LowReadII/rawdata

./run_splitFastq_fwd.sh

./run_splitFastq_rev.sh

./run_aggregate.sh

cd /project/microbiome/data_queue/seq/LowReadII/tfmergedreads

./run_slurm_mergereads.pl

cd /project/microbiome/data_queue/seq/LowReadII/otu

./run_slurm_mkotu.pl

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