Spencer1 bioinformatics

Raw reads

We received one file with sequence reads.

Demultiplexing

mkdir /gscratch/grandol1/Spencer1 /gscratch/grandol1/Spencer1/rawreads

cd /gscratch/grandol1/Spencer1/rawreads
unpigz --to-stdout /project/gtl/data/distribution/WeissLehman/Spencer1/rawreads/*.fastq.gz | split -l 16000000 -d --suffix-length=3 --additional-suffix=.fastq - Spencer1_

/project/gtl/data/distribution/WeissLehman/Spencer1/demultiplex/run_parsebarcodes_onSplitInput.pl

Alex modified the script from 16S/ITS work for splitting fastq files based on information in their info line, to different files. It is: /project/gtl/data/distribution/WeissLehman/Spencer1/splitFastq_manyInputfiles_gbs.pl and is run with run_splitFastq_gbs.sh, in the same directory. Output is in /project/gtl/data/distribution/WeissLehman/Spencer1/demultiplex.