Tools

Tools available for data analysis

BLAST - search the genome

JBrowse - view preliminary annotations

The annotation tracks under display are:

  • "CLC_annotations" is derived from a mapping of RNA reads in the CLC Genomics Workbench. The data for this was pooled from five different tissues - leaves from the sequenced individual and its mother tree, as well as flowers, roots, and cambium from the mother tree.
  • "Maker_repeats" is an intermediate output from the annotation pipeline Maker. It was trained by feeding the output of the CEGMA analysis into SNAP, which produced a Hidden Markov Model that was used in Maker. Repetitive regions and ab-initio predicted genes are visible.
  • "Cambium_transcriptome" displays genes identified in the cambium tissue of the mother tree.
  • "Flower_transcriptome" displays genes identified in the flower tissue of the mother tree.
  • "Leaf-mother_transcriptome" displays genes identified in the leaf tissue of the mother tree.
  • "Root_transcriptome" displays genes identified in the root tissue of the mother tree.
  • "Leaf-selfed_transcriptome" displays genes identified in leaf tissue of the selfed tree (the individual for which we have provided a genome sequence).

The five 'tissue' transcriptomes were all produced using the Transcript Discovery plugin in the CLC Genomics Workbench. This tool uses a mapping of RNA-seq reads against the reference genome to predict the location and structure of transcripts. Reads were then mapped back to predicted transcripts and any genes with less than 5x coverage were removed. Transcript structure information of a gene can be viewed in a new window by clicking on the annotation and scrolling down to 'Subfeatures'. If a gene has more than one transcript, these will be listed as XXX.1, XXX.2, XXX.3 etc. (e.g. gene 850 in Cambium_transcriptome consists of two transcripts; 850.1 and 850.2). The lengths and positions of all introns and exons can also be viewed in this window.

How to navigate in JBrowse

From "Available Tracks" on the left hand side, drag the tracks of interest onto the main panel to activate it (or double-click on the track label).
Zoom in and out using the magnifying glasses in the middle of the tool bar.
Move along the length of a sequence by dragging the red sliding window at the very top, by hitting the respective arrows in the tool bar, or by moving the main panel directly.
To view a different scaffold, just type its name in the white panel in the tool bar and hit "Go" (or press enter).
For more information visit the JBrowse webpage or hit the "?Help" button in the upper right corner of the browser interface.


Please note that use of these tools and the data therein is subject to our data usage policy which was agreed upon entry to this site.