All paired-end read unmatched

Infrastructure and utilities KneadData
9

I think that this issue occurs since that Illumina’s read pair indicator was seperated by a blank within the seq identifier line.
e.g.)
@A00930:290:HC5FGDSX3:3:1101:21685:1000 1:N:0:TGCGGCGT+TACCGAGG

Try a command
sed 's/ 1.*/\/1/g' < sample.R1.fastq > new.R1.fastq and
sed 's/ 2.*/\/2/g' < sample.R2.fastq > new.R2.fastq

I referred to this query.

Great Luck :blush:

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