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#look at the set of barcodes included for our samples lesscat barcodes_Lib1.tsv #check the reads grep CATG Lib01_R1.fastq | head #check where these are in our reads grep "^TCGAT" Lib01_R1.fastq | wc -l grep "^CGATC" Lib01_R1.fastq | wc -l grep "^AACCA" Lib01_R1.fastq | wc -l grep "^GCATG" Lib01_R1.fastq | wc -l #make a directory to put the resulting sample fastq files into mkdir sample_fastqs #look at the documentation for process_radtags ./process_radtags -h #execute the command to process the rad data ./process_radtags -i 'fastq' -1 Lib01_R1.fastq -2 Lib01_R2.fastq -o ./sample_fastqs/ -b barcodes_Lib1.tsv --inline_index -e 'nlaIII' -r --disable_rad_check |
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