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

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).