Need Suggestions To Set Up A Mirna Seq Pipeline

Question

[cameliaq]

Hey peeps!

I am new to bioinformatics. I have difficulty creating microRNA-seq pipeline analysis. The sequencing machine that I am using is Ion Torrent PGM. I really appreciate if I could receive some replies with regards to programs or any published papers regarding microRNA-seq pipeline.

I would also like to know what kind of filtering threshold or any parameter which I could set in the analysis programs.

Answer 1

[Pawel Szczesny]

Vendor of your sequencing hardware is providing a brief overview of such pipeline http://tools.invitrogen.com/content/sfs/manuals/CO25176_0512.pdf

In general PGM doesn't differ that much from other platforms (well, it does, but it's at the preprocessing level), so most of the tools for analysis of small RNAs such as miRNAkey or miRanalyzer (both have quite decent tutorials), will give you acceptable results.

[Istvan Albert]

thanks for pointing out these tools, I have now added them to the tools section

Answer 2

[Anthony Mathelier]

Predicting microRNAs from deep sequencing data can also be done using MIReNA or miRDeep2. MIReNA has already been proven to successfully predict miRNAs in plant [1] and declared a first-choice when predicting new miRNAs in mammals [2].

[1] Abrouk et al. Grass MicroRNA Gene Paleohistory Unveils New Insights into Gene Dosage Balance in Subgenome Partitioning after Whole-Genome Duplication. Plant Cell. 2012 May;24(5):1776-92

[2] Li et al. Performance comparison and evaluation of software tools for microRNA deep-sequencing data analysis. Nucleic Acids Res. 2012 May;40(10):4298-305