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Code Block
titleUntangle shuffled FASTQ file
seqtk seq -l0 Shuffled.fq > Shuffled_4line.fq| gawk '{if ((NR-1) % 8 < 4) print >> "Separate_1.fq"; else print >> "Separate_2.fq"}' Shuffled_4line.fq

After some operations on separate R1 and R2 FASTQ files, paired-end records will no longer be matched, and you need to eliminate records that are no longer matched.

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