Quality filtering by use of fastq_quality_filter does not clip bases within the sequence but rather rejects reads that do not meet the user defined criteria.
For instance you would want to keep reads that have more than q quality for at least p percentage of the read length.
fastq_quality_filter -q min_quality -p min_percent -i file -o outfile
You could select to trim when low quality base calls are at the last few nucleotides of your reads and to quality filter when there are more generalized quality issues.
In general, fastx toolkit tools are considered quite strict and you end up losing quite a lot of your sequences.
Other tools for trimming, adapter clipping and/or quality filtering are more gentle (such as scythe, cutadapt, etc).
Quality trimming and filtering should be performed with care, in order to actually increase the quality and quanity of what you get in the end.
Adapter removal to my opinion should be performed more vigorously.
5.8 years ago by
IV • 1.2k