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JBR Genome Browser Documentation

Coming soon...

About

JBR Genome Browser is a general purpose genome browser with integrated semi-supervised peak calling support using SPAN. Browser is optimized to work with large session containing BigWig and BigBed tracks.

Installation

See Installation section at JBR home page.

Basic Features

JBR Main Window Example:

Main browser window areas are:

• Information about current genome range and chromosome
• Actions tool bar
• Tracks panel

Information about current genome range and chromosome:

Browser Sessions

Open Files

• supported files
• open files + windows file type mask notes
• open from URL
• recommended formats BigWig, BigBed, BED-like

Go to Location

• chr location
• gene
• auto-completion

Navigation

• Zoom In/Out
• Zoom to Selection
• Scroll Left
• Scroll Right
• Move pointer

Track Options

• rename
• change color
• change height
• auto scale
• scale max, min
• Remove
• About
• Show source file

BED-like tracks

• region color
• region label
• region score column
• score as transparency label

BIGWIG tracks

• Scale - log, ..

Genes Track View

Advanced Features

Span Tuning

• annotations
• tune (menu, context menu)
• save (menu, context menu)
• annotate tutorial

Score filtering

'bed tuning'

Tracks Overlap