PAREsnip2 T-plot tool

Available from Version 4.5

The t-plot tool takes results from PAREsnip2 analysis along with the input transcriptome and degradome and enables the user to create target plots.

Running T-plot tool

In order to execute the sRNA Workbench and the T-plot tool 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 t-plot

If no options are entered, the usage instructions will be printed to the command line.

Usage:                                                                          
  java [-XmxNg] -jar /path/to/Workbench.jar -tool t-plot -pare_file path/to/pare/file -reference path/to/reference -results path/to/PAREsnip2/results [-min] minTagLength [-max] maxTagLength [-filter] true/false

Please note: any parameter surrounded by [] (e.g. [-max]) are optional. However, you must remove the [] (e.g. -max 19) when using them.

Once the tool has finished running, you need to open the R-script directory found at:

path\to\workbench\ExeFiles\R-scripts\T-plot_script.R

and run the R script either through the command line or through your preferred R development environment. This will then produce you a PDF file containing T-plots for all PAREsnip2 results in the results file.

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