The MIRO pipeline - Analysis of microRNAs using short-read deep sequencing data.
The MIRO (the miRNA omics) pipeline is a flexible and powerful tool for the analysis of miRNA (or more generall short RNA) expression using short-read deep sequencing data. In its present implementation MIRO is especially adapted for the analysis of reads generated with the Illumina sequencing platform. 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 output is furthermore compatible with software such as genome browsers and miRDeep.
Miro is available free for academic use. For a commercial licence please contact: heinz.himmelbauer at crg.es
In any case please cite:
Robert Kofler, Manuela Hummel, Juliane Dohm, Matthew Ingham, Lauro Sumoy and Heinz Himmelbauer (2009), MIRO: Analysis of microRNAs using short-read deep-sequencing data; submitted
Dowload the current MIRO release
Unpack the file in the folder of your choosing
Edit the file log/pipelog_config.txt and set the path to the MIRO log files.
This step is optional. An error message will however be issued if the log files have not been provided
Install the necessary prerequisites. Each MIRO script has individual prerequisites (mainly R 2.7.0) which will be mentioned in the documentatin
For the full functionallity of MIRO you need:
Perl 5.8 or higher
R 2.7.0 or higher
R-library geneplotter
R-library gplots
WebLogo 3.0
RNAfold
One of the following mappers: Eland, SeqMap, SOAP, Gem
Start by using the script run_Preprocessing.pl. See the documentation for this script.
We used the publicly available data published by Glazov et al. (2008) to test the MIRO pipeline. The results of this example run are available as supplementary file S2 in the publication. If you want to test MIRO please use this data and compare your results with the results published in supplementary file S2. The test data can be obtained at:
The test data setGlazov EA, Cottee PA, Barris WC, Moore RJ et al. A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach. Genome Res 2008 Jun;18(6):957-64. PMID: 18469162
Please report bugs to the email address shown below!
heinz.himmelbauer at crg.es