dc786f63faddbd66835ea45a511ea4d5a9587c4f gperez2 Tue Jul 22 16:51:26 2025 -0700 code review edits, refs #36116 diff --git src/hg/htdocs/goldenPath/help/bedMethyl.html src/hg/htdocs/goldenPath/help/bedMethyl.html index 491b668a7a5..35b57aeb213 100755 --- src/hg/htdocs/goldenPath/help/bedMethyl.html +++ src/hg/htdocs/goldenPath/help/bedMethyl.html @@ -107,57 +107,54 @@

Creating a bigMethyl custom track

Example #2

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

  1. Save this bedMethyl file to your computer.
  2. Save the autoSql files bigMethyl.as to your computer.
  3. Download the bedToBigBed utility.
  4. - Save the hg38.chrom.sizes text file to your computer. This - file contains the chrom.sizes for the human hg38 assembly.
  5. -
  6. 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 hg38.chrom.sizes bigMethyl.bb
  7. +
    bedToBigBed -as=bigMethyl.as -type=bed9+9 bedMethyl.bed https://genome.ucsc.edu/goldenPath/help/hg38.chrom.sizes bigMethyl.bb

  8. 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
  9. 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, learn how to create a URL -link to your data by looking at Example #6 on the +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.