miRNA analysis

[JQL]

I have same question. I do dog study.

[tamari]

Hi all,

I am working on microRNA seq (human) and I was wondering if there is a recommended tool for whole analysis i.e alignment, annotaion and count table output?
I used to work with miRanalyzer but it hasn't been updated for couple of years now, I have seen that there is a new tool ShortStack but it is much plant oreinted, is there soemthing else?

Thanks in advance,
Tamari