Downloading miRBase

Download miRBase has been deprecated and will be retired in a future version of the software. The latest miRBase database can be downloaded via the Reference Data Manager, from under QIAGEN Sets | Reference Data Elements | mirBase, as described in Quantify miRNA.

Download miRBase has been moved to the Legacy Tools (Image legacy_tools) folder of the Toolbox, and its name has "(legacy)" appended to it. If you have concerns about the future retirement of this tool, please contact QIAGEN Bioinformatics Support team at [email protected].

Previously, in order to make use of the additional information about mature regions on the precursor miRNAs in miRBase, you needed to use the integrated tool to download miRBase rather than downloading it from http://www.mirbase.org/

        Legacy Tools | Small RNA Analysis (Image small_rna_folder) | Download miRBase (Image download_mirbase)

This will download a sequence list with all the precursor miRNAs including annotations for mature regions. The list can then be selected when annotating the samples.

The downloaded version will always be the latest version (it is downloaded from ftp://mirbase.org/pub/mirbase/CURRENT/miRNA.dat.gz). Information on the version number of miRBase is also available in the History (Image history_16_n_p) of the downloaded sequence list, and when using this for annotation, the annotated samples will also include this information in their History (Image history_16_n_p).

Importing the miRBase data file

You can also import the miRBase data file directly into the Workbench. The file can be downloaded from ftp://mirbase.org/pub/mirbase/CURRENT/miRNA.dat.gz.

For the file to be recognized as a miRBase file, you have to select miRBase dat in the Force import as type menu of the Standard Import dialog.

Information about the miRBase dat format is provided in miRBase data file format.