bedMethyl and bigMethyl Track Format

The bedMethyl format is an extension of the standard BED 9 format used to display DNA methylation site data in a genome browser. This format is useful for base-resolution methylation data generated by bisulfite sequencing or direct methylation detection methods such as long-read sequencing. By including both methylation level and support (coverage), bedMethyl provides a detailed view of methylation across the genome.

The bedMethyl format includes the information of a BED 9 along with additional fields:

Valid Coverage: Reads with valid modification call
Percent Modified: Percent of valid calls that are modified
Modified calls: Number of calls with a modified base
Canonical calls: Number of calls with a canonical base
Other modification calls: Number of calls with a modified base, other modifications
Reads with a deletion: Number of reads with a deletion at this reference position
Low-confidence calls: Number of calls where the probability of the call was below the threshold
Reads with a base mismatch: Number of reads with a base other than the canonical base for this modification
Reads with no modification call: Number of reads aligned to this reference position, with the correct canonical base, but without a base modification call

The items are colored from 0% methylated modified (blue) to 100% (red). Hovering over an item or clicking it shows the additional details found in bedMethyl. Methylation calls are shown separately for CpG sites (m) and non-CpG (CHG/CHH) sites (h).

Creating a bedMethyl custom track

Example #1

In this example, you will create a bedMethyl custom track using bedMethyl data for the hg38 assembly.

Paste the following track line into the custom track management page for the human assembly hg38.



track type=bedMethyl name="bedmethyl example" description="bedMethyl custom track" visibility="pack"
chr21 5010053 5010054 h 0 + 5010053 5010054 255,0,0 1 0.00 0 0 1 0 0 0 0
chr21 5010053 5010054 m 0 + 5010053 5010054 255,0,0 1 0.00 1 0 0 0 0 0 0
chr21 5010215 5010216 h 0 + 5010215 5010216 255,0,0 1 30.00 0 0 1 0 0 0 0
chr21 5010215 5010216 m 0 + 5010215 5010216 255,0,0 1 30.00 1 0 0 0 0 0 0
chr21 5010331 5010332 h 0 + 5010331 5010332 255,0,0 1 70.00 0 0 1 0 0 0 0
chr21 5010331 5010332 m 0 + 5010331 5010332 255,0,0 1 70.00 1 0 0 0 0 0 0
chr21 5010335 5010336 h 0 + 5010335 5010336 255,0,0 1 100.00 0 0 1 0 0 0 0
chr21 5010335 5010336 m 0 + 5010335 5010336 255,0,0 1 100.00 1 0 0 0 0 0 0

Click the "submit" button.
Go to chr21:5,010,030-5,010,408 to see the data.

bigMethyl Format

The bigMethyl format is the indexed version of bedMethyl using bedToBigBed. See bigBed format. The bigMethyl format is more efficient to display in the Genome Browser, and it offers more trackDb options, which will allow for customization. The following autoSql definition is an example on how to specify bigMethyl files. This definition, contained in the file bigMethyl.as, is pulled in when the bedToBigBed utility is run with the -as=bigMethyl.as option.


table bigMethyl
"bigMethyl bedMethyl"
(
    string   chrom;            "Reference sequence chromosome or scaffold"
    uint     chromStart;       "Start position in chrom"
    uint     chromEnd;         "End position in chrom"
    string   name;             "dbSNP Reference SNP (rs) identifier or :"
    uint     score;            "Score from 0-1000, derived from p-value"
    char[1]  strand;           "Unused.  Always '.'"
    uint     thickStart;       "Start position in chrom"
    uint     thickEnd;         "End position in chrom"
    uint     color;            "Red (positive effect) or blue (negative). Brightness reflects pvalue"
    string   nValidCov;        "Valid Coverage"
    double   percMod;          "Percent Modified"
    uint     nMod;             "Number of calls with a modified base"
    uint     nCanon;           "Number of calls with a canonical base"
    uint     nOther;           "Number of calls with a modified base, other modification"
    uint     nDelete;          "Number of reads with a deletion at this reference position"
    uint     nFail;            "Number of calls where the probability of the call was below the threshold"
    uint     nDiff;            "Number of reads with a base other than the canonical base for this modification"
    uint     nNoCall;          "Number of reads aligned to this reference position, with the correct canonical base, but without a base modification call"
)

The first 9 fields of this bigMethyl format are the same as the first 9 fields of the standard BED format.

Creating a bigMethyl custom track

Example #2

In this example, you will create a bigMethyl file to display as a custom track.

Save this bedMethyl file to your computer.
Save the autoSql files bigMethyl.as to your computer.
Download the bedToBigBed utility.
Use the bedToBigBed utility to create a bigMethyl file from your sorted bedMethyl file, using the bedMethyl.bed file and chrom.sizes files created above.
```
bedToBigBed -as=bigMethyl.as -type=bed9+9 bedMethyl.bed https://genome.ucsc.edu/goldenPath/help/hg38.chrom.sizes bigMethyl.bb
```

Move the newly created bigMethyl file (bigMethyl.bb) to a web-accessible http, https, or ftp location. At this point you should have a URL to your data, such as "https://institution.edu/bigMethyl.bb", and the file should be accessible outside of your institution/hosting providers network. For more information on where to host your data, please see the Hosting section of the Track Hub Help documentation. Construct a custom track line with a bigDataUrl parameter pointing to the newly created bigMethyl file.
```
track type=bigMethyl name="bigMethyl Example" description="A bigMethyl file" bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigMethyl.bb visibility=pack
```
Go to chr21:5,010,030-5,010,408 to see the data.

Sharing your data with others

Custom tracks can also be loaded via one URL line. This link loads the same bigMethyl.bb track and sets additional display parameters from Example 2 in the URL:

http://genome.ucsc.edu/cgi-bin/hgTracks?ignoreCookie=1&db=hg38&position=chr21:5,010,030-5,010,408&hgct_customText=track%20type=bigMethyl%20name=Example %20bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigMethyl.bb %20visibility=pack

If you would like to share your bigMethyl data track with a colleague, you can learn how to create a URL link to your data by looking at Example #6 on the custom track help page.

Extracting data from the bigMethyl format

Because the bigMethyl files are an extension of bigBed files, which are indexed binary files, it can be difficult to extract data from them. UCSC has developed the following programs to assist in working with bigBed formats, available from the binary utilities directory.

bigBedToBed — converts a bigBed file to ASCII BED format.
bigBedSummary — extracts summary information from a bigBed file.
bigBedInfo — prints out information about a bigBed file.

As with all UCSC Genome Browser programs, simply type the program name (with no parameters) at the command line to view the usage statement.

Troubleshooting

If you encounter an error when you run the bedToBigBed program, check your input file for data coordinates that extend past the the end of the chromosome. If these are present, run the bedClip program (available here) to remove the problematic row(s) in your input file before running the bedToBigBed program.