Information & Computational Sciences

• Tablet Homepage

• Welcome to Tablet Help
• Quickstart
• The Contigs Browser
• Data Visualization
• BAM Data Visualization
• Paired-End Data Visualization
• Searching
• Overviews
• Protein Translations
• Importing Features
• Command Line Options

• Application Menu
• The Ribbon Bar
• Open Assembly
• Jump to Base
• Adjust BAM Window Size
• Tablet Options
• Subset Overview

• Allocating Memory
• What's New
• Tablet Tips

The Ribbon Bar

Home: Data

The Data Panel of the ribbon menu contains controls for importing data into Tablet.

• Open Assembly
  Select this option to display the Open Assembly dialog which allows a number of different assembly formats to be opened for viewing in Tablet.
• Import Features
  Select this option to display the Import Features dialog which allows GFF3 formatted features to be imported into Tablet.

Home: Layout Style

The Layout Style Panel contains controls which alter the display of reads within Tablet.

• Nucleotide
  Nucleotide (formerly Enhanced) colouring displays read bases using a nucleotide colouring scheme. Any variants are shown in a lighter colour, with red (rather than black) text.
• Direction
  Direction colouring displays reads using a colour scheme that colours the read according to whether it was read on the forward or reverse strand.
• Read Type
  Read Type colouring displays reads using a colour scheme that colours the read according to whether it is a single end read, the first read in a pair, or the second read in a pair.
• Classic
  Classic colouring provides a simple black on white text scheme, but enhanced slightly to help distinguish reads from the background. Variants are shown in red.
• Pack Style
  Displays a menu with the following options:
  • Packed
    Changes the display so that reads are organised into a packed layout, where multiple reads are placed on the same row, if there is room to do so.
  • Stacked
    Changes the display so that reads are organised into a stacked layout, where every read is positioned on its own row.
  • Packed (Paired End)
    As the packed layout but instead of placing multiple reads on the same row, it places multiple pairs on the same row.
  • Stacked (Paired End)
    As the stacked layout but instead or placing each read on its own row, it places pairs of reads on their own row.
• Tag Variants
  Changes the display so that bases which do not match the reference base for their base position are coloured in red on the scaled data overview.

Home: Adjust

The Adjust Panel contains slider controls for adjusting the level of display zoom and the intensity of variant highlighting.

• Zoom
  Adjusts the zoom level of the main display
• Variants
  Controls the intensity of the highlighting of read bases that are different from the consensus at that position (variant bases).

Home: Navigate

The Navigate Panel offers controls that aid in navigation.

• Page Left
  Jumps the view one screen's worth to the left.
• Page Right
  Jumps the view one screen's worth to the right.
• Jump to Base
  Opens the Jump to Base dialog, which can be used to jump the view to a specific base (padded or unpadded.
• Prev Feature
  Moves to and highlights the previous feature in the feature panel's list of features.
• Next Feature
  Moves to and highlights the next feature in the feature panel's list of features.

Home: Overlays

The Overlays Panel contains several controls for adjusting which overlays are visible when using Tablet.

• Read Info
  Toggles the display of popup information about the read currently under the mouse.
• Show Bases
  Toggles the display of text for bases in the display.
• Read Names
  Overlays the names of reads on the display. This is only available in the stacked view.
• RS Off
  Turns off the read shawowing line and read shadowing. Read shadowing highlights the reads which intersect the read shadowing line.
• RS Centre
  Enables read shadowing, with the line locked to the middle of the display.
• RS Custom
  Enables read shadowing, with the line initially following the mouse. In RS Custom mode it is also possible to lock the read shadowing line to a base position.

Advanced: BAM

The BAM Panel contains controls for adjusting - and controlling - the display of BAM data.

• Window Size
  Opens the Adjust BAM Window Size dialog, which can be used to alter the number of base positions a BAM window will display.
• Previous Window
  Moves the BAM window back to its previous location - if a previous location exists.

Advanced: Proteins

The Proteins Panel contains controls for adjusting the display of protein translations. Each button toggles the display of one of the protein translation tracks. The top three buttons control the forward translations and the bottom three control the reverse translations.

Advanced: Overview

The Overview Panel contains controls for adjusting the display of the overview. This includes options to alter the type of overview display among others.

• Scaled
  Switches the overview display to a scaled data overview mode, which shows a scaled to fit version of the data.
• Coverage
  Switches the overview display to a coverage mode which displays the coverage across the entire dataset.
• Subset
  Opens the Subset Overview Dialog allowing the alteration of the start and end bases of overview drawing.
• Reset
  Resets the overview, undoing any subsetting which has been applied.
• Coordinates
  Toggle the display of the coordinates overlay. The coordinates overlay displays the start and end points of the current overview, as well as the start and end points of the current data window.

Advanced: Components

The Components Panel contains several controls for adjusting various miscellaneous options.

• Hide Unpadded Values
  Toggles whether or not unpadded values are shown alongside their padded counterparts in the various display components.
  
• Show/Hide Overview
  Opens a menu allowing you to toggle the Overview on or off, or to select which overview visualization to display.
  
• Hide Consensus
  Toggles on or off the Consensus display panel.
• Hide Scale Bar
  Toggles on or off the Scale Bar display panel.
• Hide Coverage
  Toggles on or off the Coverage display panel.
• Hide Control Panel
  Toggles on or off the Contigs/Features/Search Control panel.

JHI Plant Bioinformatics Group