New bedMethyl and bigMethyl track type

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Gerardo Perez

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Jul 31, 2025, 6:10:37 PMJul 31

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Hello Everyone,

We are excited to announce support for a new track format for visualizing DNA methylation data: bedMethyl. This format, and its binary-indexed counterpart, bigMethyl, is designed to represent methylation calls from bisulfite sequencing or similar methods at single-base resolution across the genome.

The bedMethyl format extends the standard BED 9 format to include additional fields such as coverage, percent methylation, and the number of modified and canonical bases. When viewed in the Genome Browser, hovering over or clicking an item reveals these additional details. Items are color-coded from 0% methylated (blue) to 100% (red). Methylation calls are shown separately for CpG sites (m) and non-CpG (CHG/CHH) sites (h).

The bigMethyl format allows fast access to large methylation datasets and is ideal for displaying these tracks at scale in the Genome Browser.

For more information, see the bedMethyl and bigMethyl Track Format help page.

We would like to thank Brian Joseph Raney, Max Haeussler, and Gerardo Perez for their work developing and testing this track format.

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