Raw reads
We retrieved 12 files from the NovaSeq runs. Four of these contain the 1x100bp reads. I am not sure why we received 2 index reads for each run. The files with the raw reads of interest will be in: /project/gtl/data/raw/2Trout/1and2/rawreads.
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mkdir 2Trout1and2
cd 2Trout1and2
gunzip unpigz --to-stdout /project/gtl/data/raw/2Trout/1and2/rawreads/2Trout1and2_S1_L001_R1_001.fastq.gz cat /project/gtl/data/raw/2Trout/1and2/rawreads | split -l 16000000 -d --suffix-length=3 --additional-suffix=.fastq - 2Trout1and2_
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/project/gtl/data/raw/2Trout/1and2/rawreads/demultiplex/run_parsebarcodes_onSplitInput.pl
Recombine by sample name and mid
/project/gtl/data/raw/2Trout/1and2/rawreads/demultiplex/run_splitFastq_gbs.sh