Hi, I decided to use Trimmomatic for trimming raw reads. I saw many researchers used the inputs (LEADING:3 TRAILING:3) authors suggested on their webpage (https://www.usadellab.org/cms/?page=trimmomatic) for trimming RNA-Seq reads.
I thought these values are very low, so I started to find out their exact meaning. A website (http://drive5.com/usearch/manual/quality_score.html) used the below figure to explain the Phred (quality score), and stated that: "Note that a Q score of 3 means P (the error probability)=0.5, meaning that there is a 50% chance the base is wrong, and lower values represent even higher probabilities of error." Can anyone explain why you suggested such low criteria for filtering reads? Best, Armin