reads from miRNA-seq

Question

[Cacau]

I was curious whether reads generated from miRNA-seq can be mapped to non-miRNA genes. Does anyone know about this?

Answer 1

[Chirag Nepal]

Yes, it will map. Reads generated from miRNA-seq library (which is done by size selection) contains other RNAs in that size range which normally includes small RNAs derived RNAs (from snoRNAs, tRNA, trnasposons) and other class of RNAs (such as piwi RNAs, intronic RNAs).

Answer 2

[kanwarjag]

IS there a known work flow to work with miRNA seq data meaning which aligner to use reference genome and calculation of differential expression?

[GenoMax]

Microrna Pipeline