miRDeep

Discovering known and novel miRNAs
from deep sequencing data


Developed by Marc Friedländer and Nikolaus Rajewsky
Systems Biology group at the Max Delbrück Center, Berlin-Buch

April 4th, 2008


The miRDeep package was developed to discover active known or novel miRNAs from deep sequencing data (Solexa/Illumina, 454, ...). The package consists of everything you need to analyze your own deep sequencing data after removal of ligation adapters: a number of scripts to preprocess the mapped data, and the core miRDeep algorithm that will analyze and score these data.

 

The package is freely available for non-commercial purposes. For commercial purposes, please contact us.

 

If you use miRDeep in your scientific research, please cite us:

Friedländer, M.R., Chen, W., Adamidi, C., Maaskola, J., Einspanier, R., Knespel, S., Rajewsky, N. 'Discovering microRNAs from deep sequencing data using miRDeep', Nature Biotechnology, 26, 407-415 (2008)

 

Three compressed downloads are available at this site:

Both demo_limited and demo_full contain a README file that contains instructions how to run miRDeep on your own deep sequencing data. Running it on the demo data allows you to test that it produces what it is supposed to produce (positive control). We highly recommend to test the package on the demo data.

  1. miRDeep.tgz contains the core algorithm script and all auxiliary scripts.
  2. demo_limited.tgz contains all the files that we used to predict C. elegans known and novel miRNA, starting with the file containing the alignments of the filtered reads to the nematode genome and ending with the file of the final predictions (size of this demo: a few MB)
  3. demo_full.tgz contains all the files that we used to predict C. elegans known and novel miRNA, starting with the file containing the alignments of all reads to the nematode genome and ending with the file of the final predictions (warning: size of this file: 100 MB)

 

For questions on miRDeep, contact: friedlaender at mdc-berlin dot de

For general comments or questions on commercial use, contact: rajewsky at mdc-berlin dot de

(substitute 'at' with '@' and 'dot' with '.' to get the proper email addresses)