...
gunzip /project/gtl/seq/raw/trout1/Trout1_4/rawreads/Trout1_P4_S2_L002_R1_001.fastq.gz
cat /project/gtl/seq/raw/trout1/Trout1_1/rawreads/Trout1_P1_S1_L001_R1_001.fastq | split -l 10000000 -d --suffix-length=3 --additional-suffix=.fastq - Trout1_Pool1_
cat /project/gtl/seq/raw/trout1/Trout1_2/rawreads/Trout1_P2_S2_L002_R1_001.fastq | split -l 10000000 -d --suffix-length=3 --additional-suffix=.fastq - Trout1_Pool2_
cat /project/gtl/seq/raw/trout1/Trout1_3/rawreads/Trout1_P3_S1_L001_R1_001.fastq | split -l 10000000 -d --suffix-length=3 --additional-suffix=.fastq - Trout1_Pool3_
cat /project/gtl/seq/raw/trout1/Trout1_4/rawreads/Trout1_P4_S2_L002_R1_001.fastq | split -l 10000000 -d --suffix-length=3 --additional-suffix=.fastq - Trout1_Pool14
...
sed -E 's/^([[:alnum:]-]+),([[:alnum:]-]+),([[:alnum:]-]+).*/\1,\2,\3/' Trout1Pool4_Demux1.csv > Trout1Pool4_Demux_fixed.csv
cd /gscratch/grandol1/Trout1
Parse split files
/project/gtl/seq/raw/trout1/Trout1_1/demultiplex/run_parsebarcodes_onSplitInput.pl
...
Recombine by sample name and mid
cd mkdir Pool1 Pool2 Pool3 Pool4
mv *_Pool1* ./Pool1
mv *_Pool2* ./Pool2
mv *_Pool3* ./Pool3
mv *_Pool4* ./Pool4
/project/gtl/seq/raw/trout1/Trout1_1/demultiplex./run_splitFastq_gbs.sh
cd /project/gtl/seq/raw/trout1/Trout1_2/demultiplex./run_splitFastq_gbs.sh
cd /project/gtl/seq/raw/trout1/Trout1_3/demultiplex./run_splitFastq_gbs.sh
cd /project/gtl/seq/raw/trout1/Trout1_4/demultiplex./run_splitFastq_gbs.sh