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 @@
In this example, you will create a bigMethyl file to display as a custom track.
bedToBigBed
utility.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.bbbedToBigBed -as=bigMethyl.as -type=bed9+9 bedMethyl.bed https://genome.ucsc.edu/goldenPath/help/hg38.chrom.sizes bigMethyl.bb
track type=bigMethyl name="bigMethyl Example" description="A bigMethyl file" bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigMethyl.bb visibility=packCustom 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.
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.