Available from Version 4.6

PAREameters is a tool for the inference of plant miRNA targeting criteria using RNA sequencing data (small RNA and corresponding degradome).

A user manual for PAREameters can be found here and a set of tutorial data can be downloaded from here.

System Requirements

At the time of writing only Java 8 is currently supported.

Minimum: Java SE 8 and 6GB RAM

Recommended: Java SE 8 and 16GB RAM

PAREameters has been tested on Windows (7 and 10), Linux (Ubuntu 16.04) and MacOS (10.13). If you have any issues with the execution of PAREsnip, please let us know by email or in the comments.

Running PAREameters

Command-line analysis

In order to execute the sRNA Workbench and PAREameters 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 pareameters

If no options are entered, the usage instructions will be printed to the command line. An example of a complete instruction is given below:


java [-XmxNg] -jar /path/to/Workbench.jar -tool pareameters -pare_file path/to/pare/file -srna_file path/to/srna/file -genome_file path/to/genome/file -transcript_file path/to/transcript/file -output_dir path/to/output/directory – species_name species_name [-mirna_file path/to/mirna/file] [-config path/to/PAREameters/config/file] [-paresnip2_rules path/to/paresnip2_rules/file]

 -XmxNg (optional but recommended) gives N GB of memory to the Workbench process

Note: parameters in square brackets are optional (but the [] must be removed if you use them).

Default parameter files that can be used or edited are found in the default parameters directory of the Workbench.

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