2AMF MiSeq Bioinformatics

Owned by Gregg Randolph
Last updated: Dec 30, 2022
1 min read

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

cd /gscratch/grandol1/2AMF/rawdata

unpigz --to-stdout /project/gtl/data/raw/2AMF/rawdata/2AMF_R1.fq.gz | split -l 1000000 -d --suffix-length=3 --additional-suffix=.fastq - 2AMF_R1_ ;
unpigz --to-stdout /project/gtl/data/raw/2AMF/rawdata/2AMF_R2.fq.gz | split -l 1000000 -d --suffix-length=3 --additional-suffix=.fastq - 2AMF_R2_

//project/gtl/data/raw/2AMF/rawdata/run_parse_count_onSplitInput.pl

above step running 12-30-22

cd /project/gtl/data/raw/2AMF/rawdata

./run_splitFastq_fwd.sh

./run_splitFastq_rev.sh

./run_aggregate.sh

cd /project/gtl/data/raw/2AMF/tfmergedreads

./run_slurm_mergereads.pl

cd /project/gtl/data/raw/2AMF/otu

./run_slurm_mkotu.pl

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