The small RNA Workbench Version 4.0 ALPHA

The small RNA Workbench Version 4.0 ALPHA: Released: 04/09/2015

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This release is an Alpha test for the newest version of the workbench (check the frequently encountered problems for a list of known issues). This version comes with an early release of a new tool that will be included in the final 4.0 Workbench Release and a new look to the interface.

The workbench will slowly be completely migrating to the new interface over the coming months.

The new interface discards the old style of single tool multi document interface from Version 2 onwards to this point in favour of a workflow style. Users currently have the option to use only one preconfigured workflow, however more preconfigured options will be coming soon along with the ability to completely customise a workflow for a user’s own needs.

In addition to the new workflow a completely new backend to the program has been included, this removes all of the previous IO based in memory calculations in favour of a database module that should help to counteract some of the problems faced with memory requirements for the software. More details will be given out in a post on the workbench diaries section similar to that of the Adapter Removal low memory post.

Also some new functionality for sequence alignment has been included

General

  1. A new front end in the form of a Workflow model has been included. Users can still view the old style from the new interface by clicking the version 3.2 button and using the program as before.
  2. Bowtie can now be used from the wizard to align sequences, however, currently only pre-indexed genome files should be used in this mode. Pre indexed genomes can be found at the bowtie website: http://bowtie-bio.sourceforge.net/index.shtml

Quality Checking and Normalisation

A brand new tool for quality checking and normalisation of small RNA data. This tool works as a flow from setup through review and completion. Users can setup the software to reflect exactly how their experiment was formed, check the initial quality of the data, deselect problematic files and then normalise the results.

users can then export the data as CSV format for use in GEO uploading or as normalised FASTA files. Users can also export all of the graphs shown in the quality checking stage of the workflow. Further details can be found here

Differential Expression

A second workflow containing all of the previous normalisation and QC analysis nodes but with the addition of a differential expression node is also included. Further details can be found here

Changes to the Version 3 build…

As previously mentioned, the version 3.2 release can still be accessed from this build by clicking the “Show version 3.2” and the Version 4.0 alpha can be returned to from the tools menu.

The version 3 tools will continue to be updated until a time that they move to the new interface or are completely replaced. As such, some tools from the previous version have received improvements. Details below:

Adapter Removal

  1. Low memory version has received some back end improvements to speed of processing
  2. Low memory version has corrected errors produced when processing HD adapter samples

miRCat

  1. Users can now specify the output directory for miRCat results when running from the command line. The extra flag

    -output_directory followed by the desired location can be added to the miRCat instruction.