how to distinguish pre-mRNA and mature mRNA from my nuclear RNA-seq data?

Question

[bioinfo_wen]

AS we know, most pre-mRNAs were retained in nucleus and after processing such as alternative splicing, it was transported into cytoplasm. However, there are also some mature mRNA/lncRNA exists in nucleus. If I have my nuclear samples sequenced, how could I seperate mature mRNA and pre-mRNAs from my total sequenced reads? Because I want to know the expression level of pre-mRNA and mature mRNA, is there any tools that can solve this problem?

[Eric Lim]

This is not a bioinformatics question.

Fractionating your samples into nuclear and cytoplasmic RNA wouldn't help if you're capturing RNA via polyA plus. To answer your question, you'll need to prepare your RNA via Ribo minus.

Take a look at this paper (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4640133/) and some of the publicly deposited data to help you get started.