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How do you trim adapters for interleaved fastq files?

Open kvhardy opened this issue 5 months ago • 1 comments

I am trying to trim adapters for an interleaved fastq file. However, I use this command : fastp --interleaved_in -i 2139258.interleaved.fq.gz -o 2139258.interleaved.trimmed.fq.gz , but I keep gettin an error asking me for paired end outputs. Does this program not support an interleaved output fastq file?

kvhardy avatar Jul 22 '25 23:07 kvhardy

use -o R1.fq.gz -O R2.fq.gz if you want separated paired files, otherwise use --stdout > output.fq to get interleaved output.

sfchen avatar Jul 29 '25 02:07 sfchen