AMF1 iSeq Test Bioinformatics

Owned by Gregg Randolph
Last updated: Sept 30, 2021
1 min read

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

mkdir -p /gscratch/grandol1/AMF_Test/rawdata

cd /gscratch/grandol1/AMF_Test/rawdata

unpigz --to-stdout /project/microbiome/data_queue/seq/AMF_Test/rawdata/AMF_Test_S1_L001_R1_001.fastq | split -l 1000000 -d --suffix-length=3 --additional-suffix=.fastq - AMF_Test_R1_ ;
unpigz --to-stdout /project/microbiome/data_queue/seq/AMF_Test/rawdata/AMF_Test_S1_L001_R2_001.fastq | split -l 1000000 -d --suffix-length=3 --additional-suffix=.fastq - AMF_Test_R2_

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

cd /project/microbiome/data_queue/seq/AMF_Test/rawdata

./run_splitFastq_fwd.sh

./run_splitFastq_rev.sh

./run_aggregate.sh

cd /project/microbiome/data_queue/seq/AMF_Test/tfmergedreads

./run_slurm_mergereads.pl

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