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)

#vcf
bgzip example.vcf
CODE

#bed
bgzip example.bed
CODE

3. Create a tabix index file for the bgzip-compressed vcf or bed (example.vcf.gz.tbi, example.bed.gz.tbi)

#vcf
tabix -p vcf example.vcf.gz
CODE

#bed
tabix -p bed example.bed.gz
CODE

4. Upload both onto Synapse and enjoy Biodalliance!



Need More Help? Ask a question in the Synapse Help Forum. Your feedback is key to improving our documentation, so contact us if something is unclear or open an issue.