redone TRNL1 demultiplexing

Owned by Gregg Randolph
Last updated: Aug 29, 2022
1 min read

cd /project/microbiome/data_queue/seq/TRNL1/rawdata

dos2unix TRNL1_Demux.csv

unpigz --to-stdout /project/microbiome/data_queue/seq/TRNL1/rawdata/TRNL1_R1.fastq.gz | split -l 5000000 -d --suffix-length=3 --additional-suffix=.fastq - TRNL1_R1_
unpigz --to-stdout /project/microbiome/data_queue/seq/TRNL1/rawdata/TRNL1_R2.fastq.gz | split -l 5000000 -d --suffix-length=3 --additional-suffix=.fastq - TRNL1_R2_

cd /gscratch/grandol1/TRNL1/rawdata/

/project/microbiome/data_queue/seq/TRNL1/rawdata/run_parse_count_onSplitInput.pl

cd /project/microbiome/data_queue/seq/TRNL1/rawdata

./run_splitFastq_fwd.sh

./run_splitFastq_rev.sh

./run_aggregate.sh

 

 

 

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