Genome Browser

Biodalliance Setup

  • Species = Supports human (hg19/Gr37) and mouse (mm10/Grch38) genomes
  • chr = Chromosome number
  • viewStart = Start position
  • viewEnd = End position

Supported File Types

BIGWIG

  • Source name = Track name
  • File = synID of a bigwig file (.bw, .bigWig)
  • Height = Height of the track (pixels)
  • Color = Color of the track

VCF/BED

Note: To embed vcf and bed files, the files must be in the correct format. Please view how to prepare vcf and bed files below if they are not in the right format.

VCF (.vcf.gz AND .vcf.gz.tbi)

  • Source name = Track name
  • File = synID of a compressed vcf file (.vcf.gz)
  • Tabix file: synID of a tabix index file (.vcf.gz.tbi)
  • Height = Height of a datapoint glyph in the track (pixels)
  • Color = Color of the track

BED (.bed.gz AND .bed.gz.tbi)

  • Source name = Track name
  • File = synID of a compressed vcf file (.vcf.gz)
  • Tabix file: synID of a tabix index file (.vcf.gz.tbi)
  • Height = Height of a datapoint glyph in the track (pixels)
  • Color = Color of the track

Preparing VCF and BED Files

  1. Download and build the tabix and bgzip programs
  2. Compress your vcf or bed file using bgzip (example.vcf -> example.vcf.gz, example.bed -> example.bed.gz) {row} {column width=6}
    #vcf
    bgzip example.vcf
    

    {column} {column width=6}

    #bed
    bgzip example.bed
    

    {column} {row}

  3. Create a tabix index file for the bgzip-compressed vcf or bed (example.vcf.gz.tbi, example.bed.gz.tbi) {row} {column width=6}
    #vcf
    tabix -p vcf example.vcf.gz
    

    {column} {column width=6}

    #bed
    tabix -p bed example.bed.gz
    

    {column} {row}

  4. Upload both onto Synapse and enjoy Biodalliance!

Need More Help!

Try posting a question to our Forum.

Let us know what was unclear or what has not been covered. Reader feedback is key to making the documentation better, so please let us know or open an issue in our Github repository (Sage-Bionetworks/synapseDocs).

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