VisSR

Available from Version: 1.0

Sequence visualisation within the UEA sRNA Workbench is performed in the VisSR tool (pronounced visor). The tool may be run on its own or from other tools, e.g. miRCat. To open the tool choose ‘VisSR’ from the ‘Tools’ menu in the main Workbench window. Data is loaded into VisSR from the File menu.

VisSR showing a gene annotation for Arabidopsis thaliana

From top to bottom, the VisSR screen is divided into four sections:

Navigation controls

The sequence identifiers, e.g. chromosome ids, are shown in the drop-down list. Changing the value will load the sequence and recalibrate the display.Next to the list is an editable text-field within which base coordinates can be typed. When the two numbers are separated by a ‘-‘ the display is moved to the specified coordinates. If the numbers are separated by a ‘+’ then the second number specifies the width. Additionally, a ‘kb’ or an ‘mb’ may be included at the end of each number as short-hand for a thousand bases and a million bases respectively. For example, typing ‘1.5mb-2.5mb’ would move the display so that base number 1,500,000 lies on the left-hand side, and base number 2,500,000 on the right. The same result would be achieved by typing ‘1500kb+1mb’.Alternatively a text-based identifier can be typed and a search will be performed. This is useful for finding a specified gene when displaying annotations. For example, typing ‘AT1G01010’ when displaying chromosome 1 of Arabidopsis thalianaproduces the view shown above.The ‘<<‘, ‘<‘, ‘>’, ‘>>’ buttons move the displayed range according to the currently displayed width. The ‘<<‘ button moves the display to the left by one whole screenful, while the ‘<‘ button moves the display by half a screenful. The other buttons move the displayed range to the right.

 

Sequence overview

The sequence overview is a number line which represents the current sequence, e.g. chromosome. The red box indicates the portion of the sequence which is displayed in the main data view below. The red box can be dragged using the mouse along the number line to move the displayed region.

 

Zoom control

The current zoom level corresponds to the location of the vertical notch on the horizontal line. To zoom out or in click on the notch and drag it to the left or right. As the zoom level is increased the main data view will change accordingly. Zooming is performed relative a fixed zoom point. To set the zoom point, click anywhere in the main data view. The position is indicated by a vertical grey line. The zoom point will remain in view when zooming. Clicking on the horizontal line away from the notch will cause the zoom level to jump.

 

Main data view

The display is divided into tiers, with a label on the left and the data on the right. The sequence is displayed in the first tier. To see the bases zoom all the way in. The second tier shows the view’s position on the governing sequence. Tiers can be added to the view using the items on the File menu. Loaded data is displayed using coloured graphic items (glyphs). The glyph for a strand aligned sequence displays an arrow at one end to indicate direction. If a label has been assigned to the glyph it will be shown when the zoom level is sufficiently high. Double-clicking on a glyph will cause the display to zoom in on it. A help-tip is displayed when the mouse hovers over a glyph. A context menu is displayed when either a tier’s label or a glyph is right-clicked.
  • Carlos Pérez Arques

    Hello,

    I’m using VisSR to visualize and check strand bias in several loci of a patman file generated by Sequence Alignment (from a sRNA file and a genome file). The problem I have is that the tiers generated by VisSR containing the sRNAs sequences aligned are too big (vertical axis too long) because it shows a lot of sequences, and when I try to “take picture” of it, it doesn’t get all the sequences. With the zoom tool I can maximize or minimize the horizontal axis, but I haven’t found anything to make the vertical axis smaller. Is there some way to do this?

    Thanks in advance,
    Carlos

    • The sRNA Workbench

      Hi Carlos,

      There is no option for this at the moment. Could you take a screen grab of the issue so I can get a better understanding of what type of control you might need? You can send it to my email: matthew.stocks@uea.ac.uk

      And I will try and figure out a good way of making this work.

      Cheers,
      Matt

  • Kenlee Nakasugi

    Hello,

    I ran ta-si prediction tool, everything ran fine. When I right clicked on a locus ID in the results to view in VisSR or from the ‘View’ menu, VisSR loads the genome file, but nothing else (the ta-si information) is displayed. I’m not sure what file to load from the ‘File’ menu as none generated from the ta-si tool appears to be the correct format for VisSR. How can I load the ta-si results in VisSR?

    I’m using v2.4 of the workbench.

    Many thanks,
    Ken

    • Hi Ken,

      At times I have noticed that the code we have in place to target the desired region of the genome is not that robust. Most likely it has loaded the information but you are not taken to the correct area of the genome. Can you try to repeat your job, load in VisSR and then zoom right out using the slider (and make sure you are on the correct chromosome) when/if you find your sequences double clicking on them should automatically zoom you in.

      Let me know if this works and I will investigate the targeting problem.

      Thanks,
      Matt

      • Kenlee Nakasugi

        Hi Matt,

        I tried zooming in and out, the window is still blank in VisSR. I can send you a screenshot if you like. I’m not seeing any features being loaded. To make sure what I did was correct:
        1. I ran Ta-si prediction tool => Results window shows rows with ta-si information
        2. I right clicked on a row, and select “show in VisSR”, which then loads VisSR, which has the genome information (the chromosomes), but no other features. The same situation arises even when I select “View->Show in VisSR” from the ta-si software menu. Note my genome file chromosome headers are actually named ‘>scaffoldxxxxx sizeXXXX’

        Thanks!
        Ken

        • Hi Ken,

          Ok that is a strange one, I am at a conference in Spain at the moment so after the talks finish today I will run some tests, the first thing that springs to mind is that spaces in the FASTA headers for the scaffold are causing issues but that would surprise me to be honest.

          How many scaffolds are there? Was VisSR at least selecting and displaying the correct scaffold for your TAS locus?

          Thanks,
          Matt

          • Kenlee Nakasugi

            Hi Matt,

            Thanks for your support even though you must be very busy.

            VisSR is starting up and just loading the entire genome and not jumping to the scaffold I selected in ta-si. There are about 340,000 scaffolds, and it loads and displays scaffold1. I can then select a scaffold of interest, and can zoom all the way in and see the individual bases, but no other features even at the location where the phased reads are supposed to be.

            Is there some other file I need to preload into VisSR?

            Thanks,
            Ken

          • Hi Ken,

            No there are no extra files required. It should just work, could you email me the first 100 lines of your genome file and your small RNA file? So I can see if I can detect the problem?

            Matthew.stocks@uea.ac.uk

            Thanks,
            Matt

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