bbabbd5d2566d47d923d51dbe350634783455999 mspeir Sun Oct 26 12:14:52 2025 -0700 change soe to gi, refs #35031 diff --git src/hg/htdocs/goldenPath/help/bigWig.html src/hg/htdocs/goldenPath/help/bigWig.html index bdd1b5ac13d..144b8932403 100755 --- src/hg/htdocs/goldenPath/help/bigWig.html +++ src/hg/htdocs/goldenPath/help/bigWig.html @@ -43,38 +43,38 @@

Creating a bigWig track

To create a bigWig track from a wiggle file, follow these steps:

Step 1. Create a wig format file following the directions here. When converting a wig file to a bigWig file, you are limited to one track of data in your input file; therefore, you must create a separate wig file for each data track.

Step 2. Remove any existing "track" or "browser" lines from your wig file so that it contains only data.

Step 3. Download the wigToBigWig program from the -binary utilities directory.

+binary utilities directory.

Step 4. Use the fetchChromSizes script from the -same directory to create the +same directory to create the chrom.sizes file for the UCSC database with which you are working (e.g., hg19). If the assembly genNom is hosted by UCSC, chrom.sizes can be a URL like: -http://hgdownload.soe.ucsc.edu/goldenPath/genNom/bigZips/genNom.chrom.sizes

+http://hgdownload.gi.ucsc.edu/goldenPath/genNom/bigZips/genNom.chrom.sizes

Step 5. Use the wigToBigWig utility to create the bigWig file from your wig file:

wigToBigWig input.wig chrom.sizes myBigWig.bw

Note that the wigToBigWig program also accepts gzipped wig input files.

Step 6. Move the newly created bigWig file (myBigWig.bw) to a web-accessible http, https, or ftp location.

Step 7. If the file name ends with a .bigWig or .bw suffix, you can paste the URL directly into the custom track management page, click "submit" and view the file as a track in the Genome Browser. By default, the file name @@ -177,37 +177,37 @@

Example #3

To create a bigWig track from a bedGraph file, follow these steps:

  1. Create a bedGraph format file following the directions here. When converting a bedGraph file to a bigWig file, you are limited to one track of data in your input file; therefore, you must create a separate bedGraph file for each data track.
  2. Remove any existing track or browser lines from your bedGraph file so that it contains only data.
  3. Download the bedGraphToBigWig program from the - binary utilities directory.
    4. + binary utilities directory.
  4. Use the fetchChromSizes script from the - same directory to create the + same directory to create the chrom.sizes file for the UCSC database with which you are working (e.g., hg19). If the assembly genNom is hosted by UCSC, chrom.sizes can be a URL like - http://hgdownload.soe.ucsc.edu/goldenPath/genNom/bigZips/genNom.chrom.sizes
    5. + http://hgdownload.gi.ucsc.edu/goldenPath/genNom/bigZips/genNom.chrom.sizes
  5. Use the bedGraphToBigWig utility to create a bigWig file from your bedGraph file: 
    bedGraphToBigWig in.bedGraph chrom.sizes myBigWig.bw
    (Note that the bedGraphToBigWig program DOES NOT accept gzipped bedGraph input files.)
  6. Move the newly created bigWig file (myBigWig.bw) to a web-accessible http, https, or ftp location.
  7. Paste the URL into the custom track entry form or construct a custom track using a single track line.
  8. Paste the custom track line into the text box on the custom track management page.
    9. @@ -243,31 +243,31 @@ This dynseq display scales nucleotide characters by user-specified, base-resolution scores and was developed by the Kundaje Lab.

    Sharing your data with others

    If you would like to share your bigWig data track with a colleague, learn how to create a URL by looking at Example #6 on this page.

    Extracting data from the bigWig format

    Because bigWig files are indexed binary files, it can be difficult to extract data from them. UCSC has developed the following programs to assist in working with these files, available from -the binary utilities directory. +the binary utilities directory.