I am studying Pairend RNA-seq data. In the first step, through the FastQC tool, I checked the quality of samples. After trimming, all measurements in the FastQC report are perfect except "sequence Duplication levels".Now, I need to align them to reference genome through "bwa" aligner. Considering paired study, I want to know if "sequence Duplication levels" can bad effect on my alignment?
I appreciate it if anybody shares his/her experience with me.