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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/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