fastq_quality_trimmer

[Zimbobo]

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.

[Brian Bushnell]

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.