bed-format-generation-from-dataframe

BED-format generation from dataframe

Summary

Convert a pandas DataFrame containing genomic coordinates and annotations (such as insulation scores and boundary calls from Hi-C analysis) into BED format for downstream visualization and analysis. This skill bridges computational feature extraction and standard genome browser interchange.

When to use

You have extracted quantitative genomic features (e.g., insulation scores, boundary annotations) as a pandas DataFrame with bin coordinates and boolean or numeric columns, and need to export them as BED format for visualization in genome browsers (e.g., IGV, UCSC) or for intersection with other genomic interval datasets.

When NOT to use

• Input data is not a pandas DataFrame or does not contain coordinate columns (chrom, start, end).
• Feature columns are already in a compressed or binary format (e.g., HDF5, bigBed) — convert back to text-based BED only if re-annotation is needed.
• Coordinates are already 1-based (use conversion or validation to confirm 0-based half-open convention before writing).

Inputs

• pandas DataFrame with bin coordinates (chrom, chromStart, chromEnd columns)
• Feature columns (e.g., is_boundary_*, insulation_score, numeric or boolean annotations)

Outputs

• BED-format text file (.bed) with tab-delimited columns: chrom, chromStart, chromEnd, [name], [score], [strand]
• Validated BED file suitable for genome browser visualization and downstream analysis

How to apply

Start with a pandas DataFrame containing at minimum three columns: region/bin start coordinate, region/bin end coordinate, and a feature column (e.g., boolean is_boundary flag or numeric insulation score). Select or rename columns to align with BED format requirements (chrom, chromStart, chromEnd, and optional name/score/strand fields). Convert numeric or boolean feature columns to appropriate score values (e.g., 1/0 for boundaries or scaled insulation values). Write the DataFrame to a tab-delimited text file with .bed extension, ensuring coordinates are 0-based half-open intervals as per BED specification. Validate the output by checking that (1) row count matches input, (2) coordinate columns are numeric and properly ordered, (3) file is tab-delimited, and (4) the file can be loaded into a genome browser or validated with bedtools.