4.2 years ago by
Well, don't know if it is really a problem. normally in miRNA data, there are a bunch super highly expressed, and then the rest. That means that the time each miRNA is represented is a lot. I guess you see something weird with duplication figure as well?
Fastqc was designed for DNAseq, which you get random sequences equally represented over the genome. Something that is not true for RNAseq, and it is even worse for sRNAseq since the complexity is lower. In this cases, the expression will affect how much reads are represented. For RNAseq, at least you have different fragments from the genes. For sRNA always is the same fragment since they are small.
I would do a cumulative expression figure after you map to miRNAs and quantify to see the complexity and the number of miRNA detected, for instance. If that is ok, then I think you shouldn't be worry.