qBED

qBED: Text-Based Format for Quantitative Genomic Interval Data

qBED encodes quantitative genomic interval data, including transposon calling cards, in a standardized text-based BED-like format to support identification and analysis of transcription factor binding sites in bulk and single-cell experiments.

Key Features:

• Quantitative BED Format: Defines an open, text-based specification for representing genomic coordinates with associated quantitative values derived from transposon calling cards.
• WashU Epigenome Browser Integration: Supports direct visualization as a qBED track in the WashU Epigenome Browser (version 46 and later) for genomic context analysis.
• Flexible Dataset Support: Enables representation of additional genomic data types, including CADD scores and GWAS/eQTL hits, using the same quantitative interval framework.

Scientific Applications:

• Transcription Factor Binding Site Identification: Uses transposon calling card insertions to map and quantify transcription factor binding sites across the genome.
• Regulatory Genomics Analysis: Visualizes quantitative genomic intervals in genomic context to support studies in functional genomics, evolutionary genomics, and disease association.

Methodology:

qBED represents transposon insertion events as genomic coordinates with associated quantitative measurements in a standardized text format. These records are parsed computationally and rendered as tracks in the WashU Epigenome Browser to enable quantitative inspection and comparative genomic analysis.