FiRePat preconfigured Workflow

Available from Version 4.5

FiRePat (Finding Regulatory Patterns) is an unsupervised data mining tool for detecting sRNA-gene pairs with correlated expression levels. FiRePat is suitable for both animal and plant data. Details of the method are given in:

Mohorianu, I.; Lopez-Gomollon, S.; Schwach, F.; Dalmay, T.; Moulton, V. (2012) FiRePat – Finding Regulatory Patterns between sRNAs and putative target genes,
WIREs Data Mining and Knowledge Discovery, 2, 273-284.

FiRePat analyses can be performed either via the graphical user interface (GUI) or via the command-line.

GUI Analysis

FiRePat is a tool within the UEA sRNA Workbench. In order to run the sRNA Workbench in GUI mode, download the latest version from here and extract all the files from your downloaded zip archive to a new directory and then launch the Workbench.jar.

Next, click Open/Close menu -> Pre-configured Workflows -> Create FiRePat Workflow. Then double click on the ‘Data Input’ node.

This node is divided into three steps where the input data, processing parameters and output parameters are specified.

Step 1, specifying the input data is described here.

Step 2, specifying the processing parameters is described here.

Step 3, specifying the output parameters is described here.

The parameters can be saved in a file by clicking on ‘Save parameters’ and entering a name for the file. This file can be edited and/or used as the parameters input file when running from the command line. (The parameters will also be saved in the log file, if one is recorded.)

To start the analysis, click on ‘Open/Close Menu’ and then click on ‘Begin Workflow’.

Command-line analysis

In order to execute the sRNA Workbench and FiRePat from the command-line, navigate to the directory that you extracted the sRNA Workbench files to. Open a console window and type the following command:

java -jar Workbench.jar -tool firepat -parameters FILE

Where FILE is the full path to the parameters file. This file contains all the setup information for running the FiRaPat analysis. The parameters must be set using the parameters file, it is not possible to set them directly from the command line. A parameters file can be produced by running the workbench in GUI mode and saving the parameters to file as described above.

A suite of tools for analysing micro RNA and other small RNA data from High-Throughput Sequencing devices