TRNL Sequencing Test Bioinformatics

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

mkdir -p /gscratch/grandol1/TRNL_Test/rawdata

cd /gscratch/grandol1/TRNL_Test/rawdata

unpigz --to-stdout /project/microbiome/data_queue/seq/TRNL_Test/rawdata/TRNL_Test_S1_L001_R1_001.fastq | split -l 1000000 -d --suffix-length=3 --additional-suffix=.fastq - TRNL_Test_R1_ ;
unpigz --to-stdout /project/microbiome/data_queue/seq/TRNL_Test/rawdata/TRNL_Test_S1_L001_R2_001.fastq | split -l 1000000 -d --suffix-length=3 --additional-suffix=.fastq - TRNL_Test_R2_

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

cd /project/microbiome/data_queue/seq/TRNL_Test/rawdata

./run_splitFastq_fwd.sh

./run_splitFastq_rev.sh

./run_aggregate.sh

cd /project/microbiome/data_queue/seq/TRNL_Test/tfmergedreads

./run_slurm_mergereads.pl