The small RNA Workbench Version 4.1 ALPHA

The small RNA Workbench Version 4.1 ALPHA: Released: 22/02/2016

This release is an Alpha test for the latest version of the workbench,
Version 4.0 (check the frequently encountered problems for a list of known issues).
It includes brand new tools for quality checking, normalisation
and differential expression analysis of small RNA data.


Main fixes relating to the preconfigured pipeline for Quality Checking, Normalisation and Differential Expression

The tutorial video for this pipeline is now available and can be found here

Workflow View

  1. Interface updated to show more information about which nodes are running, correctly configured, completed and those that are waiting user input (key displayed on the interface)

File Hierarchy Wizard

  1. Replicate files now index from 1 instead of 0
  2. Multiple files can be selected when adding replicates to samples
  3. Options added for outputting aligned sequence files
  4. Bug fixes including:
    1. File removal works correctly for all file types
    2. Performance and UI improvements


Major performance improvements

File Review

  1. Users can now choose to remove ranges of size classes from the dataset using the sliders placed at the top of the interface or individual size classes using the input text box found in the options menu
  2. Bug fixes for removal of files so that it now works as expected

Report modules

  1. Performance improved greatly
  2. Export options improved
  3. Some fixes to CSS JavaFX validation problems still causing black marks to appear. Issue still remains in some plots, if unusable use the export menu to view the file in a web browser.
  4. Fixes for menu disable functionality when certain graphs are not available
  5. Jaccard Index table no longer produced for second report. Producing the data for this plot is extremely time consuming and does not add much information to the plot produced in the second report.


  1. Performance improvements
  2. Normalisation now waits for the user to press continue before running, this is to give time to select desired normalisations before the module begins

Offset Review

  1. KL divergence graph now renders more clearly
  2. If only one normalisation is selected in the previous stage the node automatically selects it
  3. Users can now control the window length (default 4000nt)

Differential Expression

  1. Fixes for some of the issues with annotation display
  2. Performance improvements
  3. Several new options for plots
    1. Fold Change cross plots
    2. MA plots
    3. Differential Expression plots