1BAT bioinformatics

I split the files for faster processing:

mkdir -p /gscratch/grandol1/1BAT/rawreads
cd /gscratch/grandol1/1BAT/rawreads
unpigz --to-stdout /project/gtl/data/distribution/Bernard/Yearout/1BAT/rawreads/23070FL-11-01-01_S1_L008_R1_001.fastq.gz | split -l 16000000 -d --suffix-length=3 --additional-suffix=.fastq - 1BAT_

Demultiplexing

Parse split files

/project/gtl/data/distribution/Bernard/Yearout/1BAT/demultiplex/run_parsebarcodes_onSplitInput.pl

Recombine by sample name and mid

/project/gtl/data/distribution/Bernard/Yearout/1BAT/demultiplex/run_splitFastq_gbs.sh