PAREfirst

PAREfirst

Available from Version 4.6

PAREfirst is a user-friendly workflow that is able to process a set of sRNAs from a high-throughput sequencing experiment to extract a subset of functional sRNAs that are used for miRNA prediction. It combines PAREsnip2 and miRCat2, which are already in the Workbench. The final output of PAREfirst is a set of predicted functional miRNAs.

A user manual for PAREfirst is available here. Also, a set of tutorial data can be found here.

 

System requirements

Minimum: Java SE 8 / 6GB RAM

Recommended: Java SE 8 / 16GB RAM

 

Starting PAREfirst

After downloading the latest version of the Workbench, you can start using PAREfirst through the graphical-user interface (GUI), or through the command-line.

Graphical user interface analysis

First, launch the Workbench.jar file to open the software home window. Next, click on ‘Open/Close menu’ to open the Workflow Menu and select the ‘Create PAREfirst Workflow’ from the ‘Pre-configured Workflows’ menu.

Then, to set up the input files, double-click on the ‘Database’ node. First, add the sRNAome file and the target analysis file, where you can either provide Degradome file or the corresponding ‘PAREsnip2 output’ file for the inserted sRNAome. Specify which type of Degradome file you inserted using the drop-down menu, and then click ‘Next’ to continue.

After that, you must provide the Genome file and the Transcriptome file, note that you can’t add the Transcriptome file if you selected ‘PAREsnip2 output’ in the previous step. Once you finished setting-up the database, click ‘Finish’ and then go back to the home window by clicking on ‘Home’ in the menu. The database node will turn into blue indicating that is ready and the rest of the Workflow nodes will appear.

The next step is to configure PAREsnip2 and miRCat2 where their nodes will be in yellow. Notice that the PAREsnip2 node will turn into yellow and you will be able to can configure it only if you provided the Degradome file. You can configure these two tools as follow:

PAREsnip2 configuration:

For PAREsnip2 configuration, double-click on the PAREsnip2 node where you can modify the configurations. Also, you may click on the ‘Default Flexible’ or ‘Default Stringent’ buttons to load the default configurations. Optionally, you can save the configuration by clicking ‘Save Parameters’. The output directory is fixed to the ‘PAREfirst data’ directory of the Workbench. After that, click ‘Next’ to set the targeting rules, where you may select to use the default Fahlgren and Carrington rules or the Allen et al. rules by clicking on the ‘Carrington Rules’ or ‘Allen Rules’ button, respectively. Optionally, you can save the selected targeting rules by clicking ‘Save Rules’. Click on ‘Finish’ to go back to the Home window where the PAREsnip2 will turn into blue. A description of PAREsnip2 configuration can be found in the PAREsnip2 manual in the UEA sRNA Workbench website.

miRCat2 configuration:

For miRCat2 configuration, double-click on its node and then open the miRCat2 setup menu and select ‘Settings’ then ‘Parameters’ to modify miRCat2 parameters. Optionally, you select ‘Animal data’ or ‘Plant data’ to load the default parameters for each, or you can load miRCat2 parameters file by clicking on ‘Load parameters’ button. The output directory for miRCat2 results will also be set to the ‘PAREfirst data’ directory of the Workbench. After that, click on ‘Continue Workflow’ then ‘Home’ buttons to go back to the home window where miRCat2 node will turn into blue. You can find detailed description of miRCat2 parameters in UEA sRNA Workbench website.

Finally, you can start the Workflow by clicking on ‘Begin Workflow’ in the Workflow menu. Once the analysis is completed, you can view the results by clicking on the ‘Results visualiser’ node, and export the t-plots, and hairpin precursors. The resulted tables of PAREfirst, PAREsnip2, and miRCat2 can be found in this directory: Workbench_directory/User/PAREfirst_Data

Command-line analysis

To start the tool from the command line, navigate to the Workbench installation directory and issue the command:

java -jar Workbench.jar -tool parefirst –config config_file

The configuration file (config_file) is in JSON format and it sets-up data for the PAREfirst workflow. A default config file can be 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