I'm relatively new to NGS analyses. I'm working with single-read ddRAD data of a non-model species and we just obtained the fastq files. The company removed the adaptors and I've just did the demultiplexing and some trimming, to remove the overhangs. When I run FASTQC and MultiQC, I obtain a high degree of duplication (around 80%). I've seen that this could be normal in RNA-seq data, but what about ddRAD? As I just started handling the data I don't think I did something wrong, but I find this high number of duplications really strange. What do you think?
Thanks in advance :) https://ibb.co/Y2LY4VH