Hello, I'm new with rnaseq and I'm having trouble deciding if I should trim or not and if yes, which tool (trimmomatic or trimgalore). I have rnaseq with mixed reads from mammalian host and bacteria, and am planning to use Trinity for de novo assembly of microbiomes. However, I need to remove the host first. Sequences are very good quality but have some adaptors and a lot of ribosomals despite the use of sortmerna. I have 2x150 pair reads. I was trying to use trimmomatic but I can't decide which parameter of minlen to use without loosing too much information, and also parameters of sliding window 4:30 but why not 10:30? or illuminaclip ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 , in which cases should I change it to 1:30:1 for example. I know there are a lot of tools for trimming, and overall I can't decide if I should even trim these sequences or removing the adapters.