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  • fastq_quality_trimmer

    Hi there,

    I am confused about the behaviour of fastq_quality_trimmer from the fastx-toolkit.

    I use it like so


    fastq_quality_trimmer -Q33 -t 28 -l 80 -i input -o output

    when I look at output with fastqc I still see in the per_base_quality box-and-whiskers plot boxed and whiskers going below 28

    I also used htseq-qa with the same result.

    My expectation was that there shouldn't be anything below 28 and reads that are trimmed from the 3' end and end with with < 80 bases are discarded.

    What am I missing?

    Thanks so much in advance.

  • #2
    Most quality trimmers implicitly assume quality increases monotonically from the end, and will stop as soon as they reach a base greater than your threshold. But quality is erratic in practice so there can still be internal bases with quality below your threshold.

    I suggest you try BBDuk, which uses the Phred algorithm for quality-trimming and yields superior results (in terms of # error bases trimmed versus # correct bases retained) compared to fastx-toolkit. There can still be bases with quality below your threshold remaining, though they will probably be more rare; the algorithm trims areas with average quality below the threshold.

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