Hello,
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
Have you checked to see how ddRAD works? If not start here and take a look at some of the papers included in that link.
Thanks for answering. I'm aware of how ddRAD works, but what I don't understand is the pattern I observe in my data. I uploaded a picture, let's see if you can check it.