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.
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.
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