sminot/demultiplex_separate_reads.sh

Last active September 10, 2019 16:37

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Demultiplex FASTQ files in which barcode was sequenced as a separate read

Raw

demultiplex_separate_reads.sh

paste -d '' <(bunzip2 -c Raw_Read2_Barcodes.fq.bz2 | awk '{if(NR % 4 == 2 || NR % 4 == 4){print}else{print ""}}') <(bunzip2 -c Raw_Read1.fq.bz2) | fastx_barcode_splitter.pl --bcfile barcodes.tsv --prefix PREFIX --suffix _R1.fastq --bol

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