How can I filter RNA-seq reads to remove reads where more than 50% of the read is low quality (Q<20)?

Question

[mar77]

I'm trying to filter out any reads that consist of more than 50% low quality reads (Q<20). I've already performed filtering steps to remove adapter contamination and remove reads with more than 10% unknown reads, both using cutadapt. Can anyone recommend a tool to use to perform this filtering step? I've previously seen NGSQC Toolkit recommended but I believe this is not supported any longer and I am having trouble accessing it.

Also I am using paired end reads so do these need to be processed together and do I need to use a tool that supports this?

Answer 1

[Papyrus]

Assuming you wanted to say " consist of more than 50% low quality bases", I would recommend fastp, it is quite easy to use and has quality filtering options for % of bases within a read not meeting a quality threshold (--unqualified_percent_limit, --qualified_quality_phred should be what you're looking for).

It handles paired-end. Personally I would do all the filtering with the same tool.

(Also, as anticipated by its name, it is quite fast).