Hello!

Recentlly, I trimmed my poor tail .fastq dataset using Trimmomatic's SLIDINGWINDOW parameter, in which I chose threshold value 15~30(i.e SLIDINGWINDOW:4:15~SLIDINGWINDOW:4:30). after, I mapped them using STAR, but I found with the increase of threshold, totally, unique and multiple mapped reads were all decreased across my 5 test_samples.

So, I'm in doubt with this situation, should it's a normal sense that my totally mapped or unique mapped reads increase with the accompany of increased trimming threshold? 

![Mapped results][1]




  [1]: https://image.ibb.co/iHOBHk/trim_star_compare.png
I would really appreciate for your helping!
Sliding window trimming is not optimal.  Because in this case there is an optimal algorithm (the Phred algorithm), I suggest you never use sliding window.  The Phred algorithm is implemented in seqtk and BBDuk.

Different aligners handle low-quality bases differently.  Quality-trimming will almost universally decrease the proportion of uniquely-mapped reads, from a given set of reads that map whether trimmed or untrimmed.  Decreasing the rate of total mapped reads generally means that you are quality-trimming too aggressively, or simply using an aligner that is not sensitive enough.  STAR is very fast, but not as sensitive as some other aligners; perhaps it does not handle the shorter reads resulting from quality-trimming very well, or perhaps it is very tolerant of low-quality bases (local aligners tend to be).

Anyway, the image would be more useful if you used optimal quality trimming and included thresholds below Q15, which is higher than is generally recommended for mapping (particularly for anything quantitative like RNA-seq).  Q10 and Q5 are worth including, and from there you can bisect if you want the optimal value.