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Load Tracks

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Roman Chernyatchik edited this page Dec 7, 2018 · 4 revisions

Load Tracks

JBR allows to visualize data in one of the following formats:

  • Signal Profile files

    • BigWig format *.bigWig, *.bw,
    • Wig format *.wig
    • IGV TDF format *.tdf

  • BED - like peaks files: *.bed

    • MACS2 peak file formats: *.broadPeak, *.narrowPeak
    • SICER peaks file formats: *.bed, *.scoreisland, *.interval
    • SPAN peak files: *.peak

  • BED file in BigBed format optimized for genome browsers: *.bigBed, *.bb

  • SPAN model files *.span

Load Track by File

  • Load signal profile track

    Use Main Menu | File | Load BigWig / Wig / BigBed file... or Main Menu | File | Load TDF file... actions.

    If your file open dialog has File Format chooser (typically on Windows, Linux)

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    ensure that you have selected desired file type. Otherwise files of this type could be not visible.

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  • Load BED-like track Use Main Menu | File | Load BED file....

  • Load SPAN model file Use Main Menu | File | Load SPAN model....

Load Track by URL

  • Use Main Menu | File | Load URL(s).....

    Supported file formats: BigWig, BigBed, BED-like files. Enter one URL or several URLs each on a new line.

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File Formats Recommendations:

  • If you want to share your session and track files on the Internet it is recommended to use BigWig file format for signal tracks (e.g. reads coverage track) and BigBed files for peak files. These formats are optimized for network access and will allow working browser smoothly.

  • JBR doesn't support large BED files with reads data. It's recommended to convert these files to reads coverage signal in BigWig format or to BigBed files.

  • For large BED-like files (more than 20 MB) with peaks data, it is recommended to convert them to BigBed format to get smoother user experience while working with JBR.

  • If you need to work with large sessions (more than 50 peaks files) it is also recommended to convert your BED-like files to BigBed format. Loading files in this format requires much less memory and you can open sessions with more than 200 files in it.

BAM files could be converted to BigWig using bamCoverage. The alternative way is to convert BAM to BedGraph using genomeCoverageBed from BedTools package. Then convert BedGraph to BigWig using bedGraphToBigWig tool from UCSC utilities.

BED-like files could be converted to BigBed using bedToBigBed tool from UCSC utilities.

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