bbabbd5d2566d47d923d51dbe350634783455999 mspeir Sun Oct 26 12:14:52 2025 -0700 change soe to gi, refs #35031 diff --git src/hg/htdocs/goldenPath/help/bedMethyl.html src/hg/htdocs/goldenPath/help/bedMethyl.html index 35624070b35..5906707d80c 100755 --- src/hg/htdocs/goldenPath/help/bedMethyl.html +++ src/hg/htdocs/goldenPath/help/bedMethyl.html @@ -106,31 +106,31 @@

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.

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.

@@ -140,39 +140,39 @@ 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.

+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 +(available here) to remove the problematic row(s) in your input file before running the bedToBigBed program.