I am looking at various options of quality trimming sequences for RNA Seq analysis

I know I can chop off a certain number of bases off the 3' or 5' ends of the reads.

Is it possible to use a sliding window to chop reads to different lengths, leaving everything above quality score 20 (for example) or would this be inadvisable as the differing lengths of reads would skew the downstream FPKM analysis?



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