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Trim Galore! removing specific adapters not present in reads

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  • Trim Galore! removing specific adapters not present in reads

    Hi, I fed a specific custom adapter sequence to trim galore on paired-end illumina files (~3B bp each), and it removed approx. 7M bases from each (--length cut-off and --quality both set to 0) . However, when I searched for direct string matches (using grep) on the fastq files, it showed no matches at all. Why did that happen? Perhaps it has to do it trim-galore's approach being more complex than simple lookup-and-cut?
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