3AMF MiSeq Bioinformatics

Owned by Gregg Randolph
Last updated: May 11, 2023
1 min read

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

cd /gscratch/grandol1/2AMF/rawdata

unpigz --to-stdout /project/gtl/data/raw/3AMF/rawdata/3AMF_S1_L001_R1_001.fastq.gz | split -l 10000000 -d --suffix-length=3 --additional-suffix=.fastq - 3AMF_R1_ ;
unpigz --to-stdout /project/gtl/data/raw/3AMF/rawdata/3AMF_S1_L001_R2_001.fastq.gz | split -l 10000000 -d --suffix-length=3 --additional-suffix=.fastq - 3AMF_R2_

//project/gtl/data/raw/3AMF/rawdata/run_parse_count_onSplitInput.pl

cd /project/gtl/data/raw/3AMF/rawdata

./run_splitFastq_fwd.sh

./run_splitFastq_rev.sh

cd /project/gtl/data/raw/3AMF/tfmergedreads

./run_slurm_mergereads.pl

cd /project/gtl/data/raw/3AMF/otu

./run_slurm_mkotu.pl

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