The UEA small RNA Workbench Version 3.0

The UEA Small RNA Workbench Version 3.0: Released: 08/07/2013

Includes: A Brand New Tool for general small RNA locus detection called CoLIde! please see the following page for further details on our new tool.

Some changes to existing tools and general software updates. All details can be found below:

Download

General Behaviour Changes

  1. C++ executable wrappers for Windows!
      • No more problems with locating java on your system, the executable wrapper will scan for java and prompt an install if it is not found. Then configure the software to run without having to configure the command line path variables
  2. .dmg OSX Style package for MAC users!
  3. Users of LINUX and other operating systems must run the software in the old way until a solution to wrapping the code up presents itself…
  4. Users will now notice there are downloads per Operating System now. This is unfortunately unavoidable if we are to provide specific wrappers for the program. However, sourceforge should recognise your OS and automatically point you to the correct version to download
  5. Added code to set the locale at run time. This is to fix any problems found by people running on a machine that is using ‘,’ for decimal points

Help Files

  1. The help files have all been updated to reflect the changes made in recent versions (long overdue!) All packaged HTML files relating to tools within the Workbench should now be up to date with new screenshots of the latest interface

STARTUP PROCEDURE

  1. Some improvements to this see a time out added to the splash screen animation for people using the workbench through X window style forwarding. The screen should now run for no more than 5 seconds then proceded to fire the workbench up

HISTORY BROWSER

  1. The history browser has been modified to update records of file usage rather than adding a new record for each file that has been added. If you access the same file from the same tool only the date and time is updated. If you update the same file from a new tool, the tool name and date and time is updated. This is to prevent multiple entries of the same file path appearing in your history
  2. The date and time format has been updated to use the local date and time for the machine that is running the workbench (previously it was locked to GMT)
  3. Added a double click to the history browser table for single file quick selection
  4. Improved the time date format stamp
  5. History can now be sorted, sorts on columns one and two are lexicographical (file name and tool name) and column three is date sorted (I expect most people will use this column for sorting mainly)

Adapter Removal

  1. Files that are processed using the Adapter Removal have their file names auto generated. These files are now all added to the history log after processing has completed
  2. Added a new option to view the size class distribution as a bar chart post processing (see the Adapter Removal pages for further information)
  3. A new check box has been added to force overwriting of files that are found in the output directory that have the same auto generated name. If the check box is not selected any files that would result in an overwrite of existing data will be ignored, a message is shown to the user and the file names are added to the general workbench log
  4. Some layout modifications to fix strangeness with the max length text box
  5. Fixed a bug that was showing all length distributions as 0
  6. Fixed a bug that would add duplicate tabs if identical files were processed more than once prior to a reset

Filter

  1. Files that are processed using the Filter have their file names auto generated. These files are now all added to the history log after processing has completed
  2. A new check box has been added to force overwriting of files that are found in the output directory that have the same auto generated name. If the check box is not selected any files that would result in an overwrite of existing data will be ignored, a message is shown to the user and the file names are added to the general workbench log

COLIDE

  1. The CoLIde program now conducts the significance test on the top 4 most abundant size classes in the putative locus (previously it was always using sizes 21-24)
  2. The CoLIde program now allows users to control the amount of offset added during the calculation of the offset Chi-Square test on the size class distribution of a locus
  3. improved the layout of the result table when maximised

TASI

  1. added new parameter to change the phasing register prior to run time. A user must modify the value in the box to view phased sequences of the defined length and phase
  2. Fixed the help when running the tool from the command line. Previously it did not mention the need for a genome (you would have received an error if the file was not found though)

SiLoCo

  1. A bug in the Export to CSV functionality has been fixed. Previously the file was always opened in “append” mode meaning that if a user selected a file for overwriting the new data would in fact be appended to the file. Now the file is blanked before new writing takes place
  2. Show locus in Genome View:
    • A bug that was causing abundances of sequences that appeared in multiple samples to be summed rather than having individual values displayed has been fixed
  3. SiLoCo now features the same context functionality as CoLIde. This includes;
    • the standard arrow view genome render
    • the aggregated view genome render 
    • the output each entire selected locus to FASTA
    • the output all individual sequence each selected locus to FASTA

miRProf

  1. The issues affecting miRProfs CSV export functionality when certain grouping options were selected have been resolved.
  2. Save parameters now also includes the miRBase version and category details in the resulting .cfg file

miRCat

  1. A hopeful solution to the hanging thread problem has been included! With any luck the zombie error that many people have been experiencing after premature ends to miRCat runs will no longer be experienced
      • I am very interested to hear of any further zombie related crashes after this release. Please inform me ASAP if you have any kind of premature program end during a miRCat run that does not close all instances of java related to the workbench!
  1. Added a proper logger to the miRCat program. Activate using the check box on the parameters window. The Logger should be completely thread safe and will track all sequences examined by miRCat and tell you why they were not classified as a miRNA (or complete details if they were). File can be found in the log directory “miRCat_Info.log”
  2. miRCat show genome view now adds a tier to display the entire miRNA locus in the VisSR visualisation

VisSR

  1. Normalised abundances generated from SiLoCo and CoLIde are now displayed properly in the tooltips
  2. VisSR can now generate the aggregated view added for CoLIde directly from aligned data files produced in the sequence alignment tool
  3. VisSR now shows the complete percentage of abundances for the 100nt windows generated for the aggregate view. Percentages are formatted to 2 s.f as are all normalised abundance values
  4. The tooltips should properly reflect those abundances that are being shown as normalised or raw counts