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How to open .BED files on Mac

To open .BED files on Mac, control-click the file and choose Open With, then use a plain-text editor to check whether it is a text-based genomic BED file.

Step-by-step instructions

  1. Control-click the file and choose Open With, then use a plain-text editor to check whether it is a text-based genomic BED file.
  2. Open genomic BED annotation tracks in IGV Desktop or load them into the UCSC Genome Browser.
  3. If the file is part of a PLINK dataset, keep the .bed, .bim, and .fam files together and use PLINK.
  4. If the file is binary and you do not know its source, ask the sender or the generating application which .BED format it uses.

Alternative methods

  • Open .BED in a browser-based viewer if desktop apps fail.
  • Try opening .BED on Mac with a secondary app to rule out app-specific issues.
  • Convert .BED only with trusted tools when direct opening is not possible.

Common issues

The .BED file opens as unreadable binary data

Not every .BED file is a text-based genomic BED file. PLINK .bed files are binary genotype tables, and IANA also registers .bed for a binary RealVNC vendor data format.

  1. Check whether the file came with .bim and .fam files; if so, open it with PLINK.
  2. Check the file source or ask the sender which application created it.
  3. Do not convert a binary .BED file by saving it from a text editor, because this can corrupt it.

A genome browser or IGV does not load the file

Genomic BED files must follow the expected column structure and must match the genome or reference assembly being viewed.

  1. Confirm the file has at least the three required BED fields.
  2. Check that columns are separated by whitespace or tabs and that there are no broken or inconsistent rows.
  3. Make sure chromosome or sequence names match the reference genome used in the viewer.

bedtools gives unexpected results

Unexpected output often comes from using the wrong .BED variant, inconsistent fields, or data that does not follow the BED specification expected by the tool.

  1. Confirm the file is a genomic BED text file, not a PLINK or RealVNC binary file.
  2. Check whether your data is BED3, BED4, BED5, BED6, or BED12 and use options appropriate for that structure.
  3. Validate a few lines manually against the BED format documentation before running large analyses.

The file is too large to open on a phone or in a basic editor

Genomic BED files can be very large annotation or interval datasets, and mobile apps or simple editors may freeze or truncate the file.

  1. Use desktop bioinformatics tools or a genome browser instead of a mobile viewer.
  2. Inspect only the first few lines with command-line tools before loading the entire file.
  3. If you only need a subset, filter or split the data with an appropriate desktop workflow.

Security note

Genomic BED files are normally plain text and do not contain macros, but malformed or extremely large files can still crash or slow down parsers and viewers.

Back to .BED extension page