Join us for a webinar: The complexities of spatial multiomics unraveled
May 2
Genomics Suite Documentation

PGS Documentation

Page tree

Versions Compared

Old Version 3

changes.mady.by.user Paul Fullerton

Saved on

compared with

New Version 4

changes.mady.by.user Paul Fullerton

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

Numbered figure captions
SubtitleTextBrowsing to location from spreadsheet with differentially expressed genes
AnchorNameBrowsing to Location

The Genome Viewer tab will open, displaying zoomed in to the selected CpG locus in CDK14 (Figure 2). 

 

Numbered figure captions
SubtitleTextViewing location in Genome Viewer
AnchorNameView at Location

The Genome Viewer visualization is composed of a series of tracks corresponding to annotation files and data files. 

  • RefSeq Transcripts 2014-01-03 (hg19) (+): transcripts coded by the positive strand
  • RefSeq Transcripts 2014-01-03 (hg19) (-): transcripts coded by the negative strand
  • Regions: by default, fold-change difference in methylation between the groups
  • Heatmap: M values for all the samples
  • Barchart: methylation levels of the selected sample (to select a sample, click on a heat map)
  • Cytoband: cytobands of the current chromosome
  • Genomic Label: coordinates on the current chromosome 

To modify a track, select it in the Tracks panel to bring up its configuration options panel below the Tracks panel. Let's modify a few tracks to improve our visualization of the data.

  • Select the Regions track, opens to Profile tab
  • Set Bar height by to Estimate
  • Set Min and Max to -10 and 10
  • Select Apply to change
  • Select Color tab
  • Set Color bars by to Fold Change (LCLs vs. B cells) (Description)
  • Select Apply to change

This will allow us to visualize the differences in methylation between the two groups.

  •  Select the Bar Chart track, opens to Y-axis tab
  • Set Min and Max to -5 and 5
  • Select Apply to change
  • Select a sample to display in the Bar Charttrack by left-clicking on a row in the heat map 

A bar indicating the M value at this probe set will appear in the Bar Chart track (Figure 3) 

The visualization
Numbered figure captions
SubtitleTextModify the tracks of the Genome Viewer to facilitate visual analysis
AnchorNameModified Genome Viewer

Image Added

The New Track button allows new tracks to be added to the viewer, while the Remove Track button removes the selected track from the viewer. Tracks can be reordered by selecting a track in the Tracks panel and dragging it up or down to move it in the list. In the Genome Viewer, select (Image Added) for selection mode and (Image Added) for navigation mode. In navigation mode, left-click and draw a box on any track to zoom in. All tracks are synced and will zoom together. Zooming can also be controlled using the interface in the lower right-hand corner of the tab (Image Added). View can be reset to the whole chromosome level using reset zoom (Image Added). Searching for a gene or transcript will also zoom directly to its location. 

The available tracks can be supplemented with a special annotation file which that can be built using a UCSC annotation file as the basis. Building and viewing the UCSC annotation file is available as an optional section of the tutorial, Optional: Adding UCSC CpG Island Annotations. 

 

Page Turner
button-linkstrue

 

Additional assistance

 

Rate Macro
allowUsersfalse