The UEA Small RNA Workbench Version 2.4.2: Released: 14/08/2012
Includes: Some changes to the behaviour of certain tools in the Workbench, some bug fixes, a small rebranding of the Workbench
- The UEA sRNA Workbench will now be referred to as the UEA Small RNA Workbench. It is the little things that count…
- The FASTA reading code has had it’s logging behaviour improved to assist in detection of invalid input sequences within the file. The abundance detection code is now more robust.
- A typo in miRBase was causing the updater to crash when requesting the latest version of miRBase to be downloaded. This has now been resolved and users should once again be able to update their database from within the software
- No more MAC OSX screen menus? I have had to disable the screen menu from the small RNA Workbench. This is because under apples code for this type of menu lies a very old rendering system that will not support any kind of enhancements to the text that can be displayed on menus. A request has come in for much more information to be given on the many acronyms used for all the tools in the Workbench to make it easier for users to decide which tool they should be loading. Until apple decide to update this area of their UI or another solution presents itself a standard menu system will be used so that I can answer this request by adding more information to the tools menu. This will not affect LINUX or Windows users
- Many of the tools used a “go to VisSR” option on their right click menus. This has hopefully been made a little clearer to new users by replacing the text with “show genome view”
- The show in VisSR buttons available from the right click menu and the drop down menu both opened a window showing tiers for positive and negative phased sRNAs. The bottom tier showed all sRNAs in the locus. A new tier has now been added to show only unphased sRNAs below the negative and positive. The lowest tier still reports all sRNAs within the locus
- When using the drop down menu to show all TA-SI loci the VisSR view will now focus on the first locus in the list
- The tier colours were making distinguishing between which values belong to which tier difficult to identify due to the very light grey colour used for each tier. In an attempt to address this the alternating tiers will now be coloured workbench grey. Some small changes to this colouring may occur in the future depending on feedback
- The zoom to code was not working correctly. All tools that require focus on a particular region in the genome (such as TASI’s show in VisSR function) should now function correctly
- A bug preventing the pipeline activation from within the miRCat start new project menu has been resolved. Users should now be able to filter and trim input data using this menu.
- Fixed a typo in miRCat output
- miRCat GUI has been redesigned slightly to match the other tools in the Workbench. It now has standard start and cancel buttons on the main interface in the same place as the other tools. The start miRCat button has been removed from the parameter browser to reflect this
- miRCat has some changes to it’s default parameters for animals to improve the accuracy of the prediction.
- minimum abundance is now 5
- locus distance is now 30
- GC content is now 30%