1TANK test bioinformatics

Raw reads

The files with the raw reads of interest will be in: /project/gtl/data/raw/2Trout/1and2/rawreads.

Swap out “distribution” for “raw” for starting directory.

Unzip and split

cd /gscratch/grandol1/

mkdir 1Tank6-1

cd 1Tank6-1

unpigz --to-stdout //project/gtl/data/distribution/TANK/1TANK/6-1/rawreads/1TANK6-1_S1_L001_R1_001.fastq.gz | split -l 16000000 -d --suffix-length=3 --additional-suffix=.fastq - 1Tank6-1_

Demultiplexing

cd /gscratch/grandol1/1Tank6-1

Parse split files

/project/gtl/data/distribution/TANK/1TANK/6-1/demultiplex/run_parsebarcodes_onSplitInput.pl

Recombine by sample name and mid

/project/gtl/data/raw/2Trout/1and2/rawreads/demultiplex/run_splitFastq_gbs.sh