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Formats

.bed, .gff, .gff3, .gtf, .vcf, .wig and .bedgraph. A .gff file is read as GFF3. Alignments (BAM, CRAM) and binary tracks (bigWig, bigBed) don’t open in BioBase.

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Choosing the assembly

Choose the reference from the Genome assembly menu. Human GRCh38 is the default.
  • Human · GRCh38
  • Human · GRCh37
  • Mouse · GRCm39
  • Mouse · GRCm38
  • Rat · mRatBN7.2
  • Zebrafish · GRCz11
  • Fruit fly · dm6
  • C. elegans · WBcel235
  • Yeast · R64-1-1
The viewer shows only the contigs your file uses. Where a contig matches the selected assembly, with or without the chr prefix, it takes the assembly’s length, or your records’ extent if that is longer, so 1 and chr1 both map to chromosome 1. A contig the assembly doesn’t list is sized from your records. The banner states the count: “Showing the N contigs in this file. Contig lengths follow the selected assembly where identifiers match.” The assembly tables are built into BioBase and carry contig lengths only, so the viewer draws your track without reference sequence or gene annotation. The view opens on the contig with the most records, framed on the span those records cover.

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Messages

“No genomic coordinates were found in this file, so there is nothing to place on a genome.” BioBase found no records with a contig and a coordinate, for example a file holding only headers or comments. “This track could not be placed on a genome. Its records may use coordinates this viewer cannot interpret.” The file has contigs and coordinates, but the track failed to draw. Select Source to check its records.