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Info |
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Status (09 Nov 2022)
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Nothing below here has been done yet
Demultiplexing and splitting
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RG_SP_500_S1_R1_001.fastq.gz
RG_SP_500_S1_R1_001.fastq.gz
Demultiplexing
The work is done by run_parse_count_onSplitInput.pl
. As the name implies, we split the raw data into many files (492), so that the parsing can be done in parallel by many nodes. The approximate string matching that we are doing requires ~140 hours of CPU time, so we are splitting the task across many jobs. By doing so, the parsing takes less than one hour.
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Code Block |
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mkdir -p /gscratch/grandol1/NS55FB1_ContamTest/rawdata cd /gscratch/grandol1/NS55FB1_ContamTest/rawdata unpigz --to-stdout /project/microbiome/data_queue/seq/NS55FB1_ContamTest/rawdata/RG_SP_500_S17-5FB1-take3_S1_L001_R1_001.fastq.gz | split -l 160000001000000 -d --suffix-length=3 --additional-suffix=.fastq - NS55FB1_R1_ ; unpigz --to-stdout /project/microbiome/data_queue/seq/NS55FB1_ContamTest/rawdata/RG_SP_500_S1_7-5FB1-take3_S1_L001_R2_001.fastq.gz | split -l 160000001000000 -d --suffix-length=3 --additional-suffix=.fastq - NS55FB1_R2_ |
making 240 10 R1 files and 240 10 R2 files, with structured names (e.g., for the R1 set):
/gscratch/grandol1/NS55FB1_ContamTest/rawdata/NS55FB1_R1_000.fastq
/gscratch/grandol1/NS55FB1_ContamTest/rawdata/NS55FB1_R1_001.fastq
etc.
run_parse_count_onSplitInput.pl
also writes to /gscratch
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NS5_Demux.csv
is used to map MIDS to sample names and projects.
Nothing below here has been done yet
Splitting to fastq for individuals
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