Computational Neural
Data and Dynamics Lab

UCSD Cognitive Science

Eran A. Mukamel, PI

A user guide for the AnnoJ epigenome browser

The AnnoJ browser displays epigenomic data, including base-resolution DNA methylation (methylC-Seq/whole genome bisulfite sequencing), RNA-Seq, ChIP-Seq, as well as annotations. Credits: The AnnoJ browser was created and developed by Julian Tonti-Filippini (2007-2009), Tao Wang (2010-2012), Huaming Chen (2013-2016) and the lab of Joseph Ecker (Salk).

Hover over the AnnoJ browser screenshot below to see information about the parts

• Annotation track: Gene bodies are indicated on the +/Watson strand (top) and on the -/Crick strand (bottom). Gray lines show introns, green boxes are exons, and arrows show the gene's 3' UTR.


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• mCG track: Each track shows pooled DNA methylation data from all single cells in one cell type cluster. Green ticks show the location of CG sites on the +/Watson strand (top) and on the -/Crick strand (bottom). The height of each tick corresponds to the level of methylation, estimated using the fraction of non-converted bisulfite sequencing cytosines.

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• mCG track: Each track shows pooled DNA methylation data from all single cells in one cell type cluster. Blue ticks show the location of non-CG sites (CH) on the +/Watson strand (top) and on the -/Crick strand (bottom). The height of each tick corresponds to the level of methylation, estimated using the fraction of non-converted bisulfite sequencing cytosines."

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• mCH track: Each track shows pooled DNA methylation data from all single cells in one cell type cluster. Blue ticks show the location of non-CG sites (CH) on the +/Watson strand (top) and on the -/Crick strand (bottom). The height of each tick corresponds to the level of methylation, estimated using the fraction of non-converted bisulfite sequencing cytosines."

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• Track selection: Drag tracks up and down to change their display order. Double click a track to toggle its visibility. Inactive (invisible) tracks are listed below the active tracks.

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• Cursor mode: Select a cursor mode: Browse (pan the view left and right), Zoom (change horizontal scale), Scale (change the vertical scale for each track), Resize (change the height of each track).