Conserved and novel miRNA analysis

Question

[Lucrezia]

Hello,

I work with a non model organism (fish) and I am approaching miRNA analyses for the first time. Most of the papers I have read remove tags that align to exons, introns and repeat sequences of the reference genome, and use the unaligned tags to identify conserved and novel miRNAs. Could anyone please explain me why they remove these tags? I have read that a good proportion of miRNAs originates from intronic and exonic regions of other genes, so why should we get rid of them?

Thanks!

[biofalconch]

Hi, where did you read this approach? I could recommend using ShortStack, it could help you with identification of microRNAs, it is not based on excluding/including any regions of the genome rather than checking if the short sequences have microRNA-like features. Hope it helps