The small RNA Workbench Version 3.2: Released: 20/05/2014
A new version of an existing tool has been added to this version as a beta. Details are below. Also includes bug squashing and general software updates. All details can be found below:
- A more informative message is now given to the user and written to the log if the input file has bad formatting or invalid lines that will cause the software to crash
- A fix for GA tracking data initialization occasional crashes from the command line
Adapter Removal LM (Low Memory)
The first in a set of major changes to the underlying data structure of the sRNA Workbench. Memory was becoming a major issue so our focus switched toward strategies for counteracting the large volumes of data our users wanted to process using the workbench. The new Adapter Removal tool (currently shown as Adapter Removal LM beta) can be used in exactly the same way as the old tool with one change, the users will notice a redundant version of the direct FASTQ to FASTA conversion in their output directory. Further details can be found in the new series of diary posts I will be making for the new tools. The adapter removal low memory diary can be found here.
Adapter Removal (All Versions)
- The GUI no longer outputs HD stats if the HD adaptor trimming option was not selected
- Users now have the option to change the background colours and colours of the glyphs used to represent; GFF annotations, Aligned small RNA files (including the aggregated mode) and the backgrounds of all tiers to suit their usage. Users should use the help->settings menu on the VisSR panel to change the colours they are interested in.
- A new version of Ghost Script has been included that no longer requires an X11 build to be present on OSX computers (as support for X11 was removed in Mountain Lion)
- A bug that left a hardcoded value in place for the offset absolute differential expression value has been fixed
- Rounded P values that read 0 have now been replaced with a more informative message. Remaining P values have been rounded to two significant figures
- The CLI output now matches the updated output style created for the GUI mode
- Fixed an issue in GUI mode where genome matches were not being summed up correctly
- Fixed an issue where normalised counts were being summed over rows incorrectly