bbabbd5d2566d47d923d51dbe350634783455999 mspeir Sun Oct 26 12:14:52 2025 -0700 change soe to gi, refs #35031 diff --git src/hg/htdocs/goldenPath/help/interact.html src/hg/htdocs/goldenPath/help/interact.html index 48c37b47bde..e3a94105071 100755 --- src/hg/htdocs/goldenPath/help/interact.html +++ src/hg/htdocs/goldenPath/help/interact.html @@ -202,40 +202,40 @@ After the file loads in the Genome Browser, you should see a number of interactions, all arching as hills instead of valleys, with some curved and many rectangular indicating a connector to a region outside of the browser window. Press the 10x zoom out button to see the full connections.

Example #4

In this example, you will use an example BED file to create a bigInteract file, allowing the data to be remotely accessed and exist within a track hub. The track settings for bigInteract on a hub can be viewed here.

  1. Download the example file here.
  2. Download the fetchChromSizes and bedToBigBed programs from the - utilities directory appropriate to your + utilities directory appropriate to your operating system.
  3. Use fetchChromSizes to create a chrom.sizes file for the UCSC database you are working with (hg19 for these examples). Alternatively, you can download the chrom.sizes file for any assembly hosted at UCSC from - our downloads page (click on "Full + our downloads page (click on "Full data set" for any assembly). For example, the hg19.chrom.sizes file for the hg19 database is located at - http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.chrom.sizes.
    4. + http://hgdownload.gi.ucsc.edu/goldenPath/hg19/bigZips/hg19.chrom.sizes.
  4. Save the autoSql file interact.as to your computer. If you want the column labels to reflect non-directional interactions, you can change the default variable names from 'source...' and 'target...' to 'region1...' and 'region2...'.
  5. Run bedToBigBed to create the bigInteract file: 
    
 bedToBigBed -as=interact.as -type=bed5+13 interactExample4.inter.bed hg19.chrom.sizes interactExample4.inter.bb
  6. Move the newly constructed bigInteract file to a web accessible http, https, or ftp location.
  7. Construct a custom track line with a bigDataUrl parameter pointing to the newly created bigInteract file. 
    
 track type=bigInteract name="interact Example Four" description="A bigInteract file" useScore=on bigDataUrl=/interactExample4.inter.bb visibility=pack 
 browser position chr3:63,820,967-63,880,091
  8. To fully take advantage of creating a bigInteract file, create a Track Hub and @@ -270,37 +270,37 @@ each interact arc. In the below image, the box column2 represents the left foot of each arc while the box column3 represents the right foot of each arc. The second row of the example data denotes an interaction to another chromosome, chr20, and thus is not represented by an arc.

    Sharing your data with others

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

    Extracting data from the bigInteract format

    Because bigInteract 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.

    As with all UCSC Genome Browser programs, one can 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 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.