The MIRO (the miRNA omics) pipeline is a flexible and powerful tool for the analysis of miRNA (or more generall short RNA) expression using the Solexa-technology. MIRO allows to preprocess the Solexa-reads, map them flexibly to several reference genomes using one of four different mappers, create differential gene (miRNA) expression profiles and cluster reads using one of several algorithm. MIRO furthermore provides compatibility to several applications such as the UCSC-genome browser and MirDeep (for discovery of new miRNAs).

At the moment MIRO consists of 24 distinct perl scripts. Following a detailed list of the individual scripts with links to detailed documentation for each.


Main scripts

Gene (miRNA) expression profiling

Clustering of the reads by mapping position

Converter for other applications

Utility tools


Generally usage of the MIRO pipeline has three levels (i) Preprocessing (ii) Mapping and (iii) Postprocessing. The general philosophy is to reduce the number of output and input files as much as possible. Therefore the output of preprocessing can be used with every mapping script and the output of every mapping script - irrespective of the used mapper - with every postprocessing script.

Typical use of MIRO will thus proceed in three steps


Convert Solexa reads into a fasta file (+aggregate identical reads and remove low complexity sequences)


Map the preprocessed fasta reads to a reference genome and convert the mapping output to a file format which is independent of the used mapper. This facilitates an easy switching of mapping tools and usage of the mapping output with every postprocessing script.


In general encompasses handling of the mapping output. At this step you may for instance convert the mapping output into a bed file or create a differential miRNA expression profile.


All scripts require:

Perl 5.8 or higher

Please see the documentation of each script for specific requirements.


Robert Kofler

Manuela Hummel

Juliane Dohm

Ana Vivancos

Matt Ingham

Lauro Sumoy

Heinz Himmelbauer


robert.kofler at