The UEA Small RNA Workbench Version 2.4.2

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

GENERAL

  • 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”

TA-SI PREDICTION

  • 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

VISSR

  • 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

MIRCAT

  • 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.
    1. minimum abundance is now 5
    2. locus distance is now 30
    3. GC content is now 30%

 

 

  • Raja

    Hi Matthew:
    I request for your suggestions.

    1. I wish to process nearly 24 wheat miRNAs datasets (illumina generated) using UEA SRNA WORKBENCH.

    I have a 64-bit pc with 4GB RAM. I don’t have a reference genome in wheat. Anyhow, I wish to use ‘Helper tool-Filter’ to process the reads based on length and abundance free of tRNA/rRNA using functionalities of your workbench.

    When I tried, the workbench shows that it reads the sRNA reads and within a few seconds, it shows the status, ‘completed successfully’. But no results are available either on the screen or in the folder.

    Hence I thought requesting your help. Whether I can use the Bam or FastQ files directly or I need Fasta files.

    2. Whether I can process without a reference sequence?

    3. Whether I can normalize reads as ‘read count per million reads’ using UEA sRNA workbench.

    Thanks,
    Raja

    • Hi Raja,

      (I also received your email but I will reply here if that is ok so others can read in case they are also having a similar issue)

      You may have encountered an error while processing although I would have thought the program will inform you if it did.

      So I can attempt to detect the problem, could you email me the first few hundred lines of the exact file you entered (to my UEA address that you emailed previously) into the workbench and also the settings you had selected when you hit run.

      The majority of filtering does not require a reference genome (unless you want to filter out genome matching reads!).

      However, normalisation using RPM will require a reference genome because you require a mapped count of small RNA reads. The only option with no genome is to normalise based on total reads in the sample (be careful with this because you cannot be sure what data you are normalising!)

      We do not at present offer a direct normalisation tool (although many of the tools will normalise data prior to processing, such as SiLoCo and miRProf and provide you with normalised data). We will be looking to add a tool for multiple normalisation methods in the near future

      I am currently adding “batch mode” functionality to the workbench for many of the helper tools that will hopefully make your life a little easier. This will be included in the next release.

      Best wishes,
      Matt

  • Airong Wang

    I want to try your this software to do some thing,Thank you for your software!

  • yang fei

    I want to use your this software to do some thing,Thank you for your software!

  • yang fei

    Thank you for your software!