AMF1 MiSeq Bioinformatics

Owned by Gregg Randolph
Last updated: Oct 22, 2021
1 min read

salloc --account=microbiome -t 0-05:00

cd /gscratch/grandol1/AMF1/rawdata

unpigz --to-stdout /project/microbiome/data_queue/seq/AMF1/rawdata/AMF1_Pool2_S1_L001_R1_001.fastq | split -l 1000000 -d --suffix-length=3 --additional-suffix=.fastq - AMF1_R1_ ;
unpigz --to-stdout /project/microbiome/data_queue/seq/AMF1/rawdata/AMF1_Pool2_S1_L001_R2_001.fastq | split -l 1000000 -d --suffix-length=3 --additional-suffix=.fastq - AMF1_R2_

//project/microbiome/data_queue/seq/AMF1/rawdata/run_parse_count_onSplitInput.pl

cd /project/microbiome/data_queue/seq/AMF1/rawdata

./run_splitFastq_fwd.sh

./run_splitFastq_rev.sh

./run_aggregate.sh

cd /project/microbiome/data_queue/seq/AMF1/tfmergedreads

./run_slurm_mergereads.pl

cd /project/microbiome/data_queue/seq/AMF1/otu

./run_slurm_mkotu.pl

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