how to use mirdeep2 without a small RNA library

Question

[Beatriz]

Hello everyone,

I'm currenly working on a project where collecting tissue samples would be almost imposible... so we have to work with public data (reference genome and the RNA seq data that is already avaliable) and from what I've seen mirdeep2 is one of the best tools to find conserved miRNA and predict novel miRNA... So I'm currrently wondering if I would be able to use this software without a small rna seq library, or if I could do a small rna seq library based on the public data that I've mentioned.

Thank you for taking your time to help this newbie, I really like miRNAs but some stuff are just hard to understand at first.

Answer 1

[Trivas]

Short answer: no. Small RNA-seq library prep kits have a specific chemistry to add sequencing adapters and also undergo a size selection using a gel. Most times, normal bulk RNA-seq libraries undergo a bead clean-up which would remove those small fragments corresponding to miRNAs. Essentially, miRNAs will not be well represented in a normal bulk RNA-seq library.

[Beatriz]

Do you have any idea on what would be a good 100% in silico methodology then? Thank you for your help.