miRNA quantification on custom database

Question

[pbigbig]

Hi everyone,

At the moment, I have some small-RNA enriched sequencing data from disease samples, read length is around 20-30 bp, tRNA largely dominated the datasets.

Could you please suggest any tool(s) or tutorials for:

• Extract and assemble for only miRNA or pre-miRNA

• Identify and quantify miRNA against a custom build database of miRNA

• Differential expression tools that is tailored for miRNA (if any)

I am totally new to this analyses, so all comments are greatly appreciated! Thank you very much in advance for your help.

[Buffo]

I recommend you to read the mirdeep2 article, it is probably one of the most widely used pipeline to analyze smallRNAseq data.

[pbigbig]

Thank you, I will check it