Pipeline for small RNA-seq data analysis of non-model organism

Question

[Reza]

Hi. How to do an analysis of a set of small RNA-seq data (Illumina) without a reference genome for identification and differential expression of conserved and novel miRNAs?

Thank you

[Buffo]

after cleaning (adapters) and filtering (quality) you can map your reads to mirbase (mature and hairpin) in the sense that most miRNAs are conserved acrooss species, it would be an interesting first approach.

Answer 1

[Hussain Ather]

Trinity has been shown to work without a reference genome.