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One-liners for fastq files

Fastq file의 앞부분에서 1만 read(40,000 라인)를 추출하기

$ head –n 40000 BL21-20x_1.fastq > small_1.fastq 또는
$ awk 'NR == 1, NR == 40000 BL21-20x_1.fastq > small_1.fastq

Interleaved file을 2개의 paired file로 분리하기

$ awk 'BEGIN{OFS="\n"} $2~/^1:/{header = $0; getline seq; getline qheader; getline qseq; print header, seq, qheader, qseq}' interleaved.fastq > file_1.fastq
$ awk 'BEGIN{OFS="\n"} $2~/^2:/{header = $0; getline seq; getline qheader; getline qseq; print header, seq, qheader, qseq}' interleaved.fastq > file_2.fastq 또는
$ sed -n '/1:N/{N;N;N;p;}' interleaved.fastq > file_1.fastq
$ sed -n '/2:N/{N;N;N;p;}' interleaved.fastq > file_2.fastq

Fastq file을 single-line fasta file로 변환하기

$ awk 'NR%4 == 1 {a=substr($0,2)} NR%4 == 2 {print ">" a "\n" $0}' file.fastq > single_line.fasta