1SUCK bioinformatics

Owned by Gregg Randolph
Last updated: Apr 26, 2023
1 min read

I split the file for faster processing:

mkdir -p /gscratch/grandol1/1SUCK/rawreads cd /gscratch/grandol1/1SUCK/rawreads unpigz --to-stdout /project/gtl/data/raw/1SUCK/rawreads/1SUCK_S1_R1_001.fastq.gz | split -l 16000000 -d --suffix-length=3 --additional-suffix=.fastq - 1SUCK_

Making 236 files

Demultiplexing

cd /gscratch/grandol1/1SUCK/rawreads/

Parse split files

/project/gtl/data/raw/1SUCK/demultiplex/run_parsebarcodes_onSplitInput.pl

Recombine by sample name and mid

/project/gtl/data/raw/1SUCK/demultiplex/run_splitFastq_gbs.sh

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