1Brose bioinformatics

I split the files for faster processing:

mkdir -p /gscratch/grandol1/Brose1/rawreads
cd /gscratch/grandol1/Brose1/rawreads
unpigz --to-stdout /project/gtl/data/raw/Brose1/rawreads/Brose1_S1_R1_001.fastq.gz | split -l 16000000 -d --suffix-length=3 --additional-suffix=.fastq - Brose1_

Making 91 files

Demultiplexing

Parse split files

/project/gtl/data/raw/5Trout1Exp/demultiplex/run_parsebarcodes_onSplitInput.pl

Recombine by sample name and mid

/project/gtl/data/raw/RHIR1/demultiplex/run_splitFastq_gbs.sh