TRNL1 demultiplexing/basic sequencing check

/project/microbiome/data_queue/seq/TRNL1/rawdata

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

cat TRNL1_T_16S_Pool_S1_L001_R1_001.fastq.gz TRNL1_T_16S_Pool_S1_L002_R1_001.fastq.gz > TRNL1_R1.fastq.gz

cat TRNL1_T_16S_Pool_S1_L001_R4_001.fastq.gz TRNL1_T_16S_Pool_S1_L002_R4_001.fastq.gz > TRNL1_R2.fastq.gz

mkdir -p /gscratch/grandol1/TRNL1/rawdata

cd /gscratch/grandol1/TRNL1/rawdata

unpigz --to-stdout /project/microbiome/data_queue/seq/TRNL1/rawdata/TRNL1_R1.fastq | split -l 10000000 -d --suffix-length=3 --additional-suffix=.fastq - TRNL1_R1_ ;
unpigz --to-stdout /project/microbiome/data_queue/seq/TRNL1/rawdata/TRNL1_R2.fastq | split -l 10000000 -d --suffix-length=3 --additional-suffix=.fastq - TRNL1_R2_

//project/microbiome/data_queue/seq/TRNL1/rawdata/run_parse_count_onSplitInput.pl

cd /project/microbiome/data_queue/seq/TRNL1/rawdata

./run_splitFastq_fwd.sh

./run_splitFastq_rev.sh

./run_aggregate.sh