Using data sets in multiple tools. The History Browser

You will notice from Version 2.3.3 of the UEA sRNA Workbench that there is a new button added to the file open dialogs when running the tool in GUI mode.

This will allow you to access your file history throughout your time using the sRNA Workbench. From here you can look at and select any files that have been accessed or created by other tools in the workbench.

The history browser

you can see which tool created or accessed the file and when this happened. You can then simply select the file (or in some tools select multiple files) and use it in the next tool as part of you analysis pipeline.

Multiple files are selected by holding CTRL (windows/LINUX) or CMD (Mac OSX) and using the mouse to click on each file you are interested in.

The history browser lists files in the order that they were last used. The history browser will only show relevant files for the type of file you are looking for (e.g. sRNA files or Genome Files)

  • Abdul Rawoof

    Hi….
    Its really nice tool but when I am using it for my data it showing alignment is complete to reference genome but it’s not giving output.
    I am using pre miRNA sequences in fasta format file and “mrna.fa” of human form ucsc “http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/” as a reference genome.

    Please could anyone guide me what should I do??

    Thanks,
    Abdul Rawoof

    • Hi Abdul,

      Thanks 🙂

      Just a quick one to begin with, is the file you downloaded still compressed?

      Cheers,
      Matt

  • Gobind Ram

    I would like to use this workbench for small RNA analysis

  • Gobind Ram

    I is a wonderful workbench. I would like to use various tools for snRNA analysis

    • Hi,

      It really depends on what type of analysis you are intending on doing. You could for example use the filter tool in reverse to identify your snRNA from your input data set in the following way:

      1. download the latest RFAM file
      2. parse the file to retain only snRNA sequences
      3. load the input data set into the filter tool and your new snRNA file into the genome box
      4. ask the tool to filter out reads that do not match to the genome (which is in fact your snRNA RFAM file)

      this would then tell you which of your sequences align to known snRNAs found in RFAM.

      If you need further information on this please let me know.

A suite of tools for analysing micro RNA and other small RNA data from High-Throughput Sequencing devices