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mkdir -p /gscratch/grandol1/RHIR1/rawreads cd /gscratch/grandol1/RHIR1/rawreads unpigz --to-stdout /project/gtl/data/raw/RHIR1/rawreads/RHIR1.fastq.gz | split -l 16000000 -d --suffix-length=3 --additional-suffix=.fastq - RHIR1_ |
Making 236 files
Stopped Here on 05-19-2022
Demultiplexing
In /project/gtl/data/RHIR1/rawreads/ I removed extraneous spaces in the file that maps MIDS to individual identifiers (RHIR1_Demux.csv). I made a fixed version (now we have RHIR1Demux_fixed.csv):
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sed -E 's/^([[:alnum:]-]+),([[:alnum:]-]+),([[:alnum:]-]+).*/\31,\12,\23/' RHIR1_Demux.csv > RHIR1Demux_fixed.csv |
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