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:
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.