I want to do some quality control on raw fastq files by doing adapter trimming and quality trimming. I'm wondering what is a good read length cutoff to use to keep a trimmed reads? i.e. if after trimming, the read is discarded if its length is smaller than a cutoff.
Similar thing, what quality score cutoff should I use to trim off bad quality reads? Is 20 a good start? And is it a good idea to do quality trimming? Many aligners have quality considered so I'm not sure which option is better.