bbabbd5d2566d47d923d51dbe350634783455999 mspeir Sun Oct 26 12:14:52 2025 -0700 change soe to gi, refs #35031 diff --git src/hg/htdocs/goldenPath/help/bigChain.html src/hg/htdocs/goldenPath/help/bigChain.html index 21b28bc0e6b..d1fba62c819 100755 --- src/hg/htdocs/goldenPath/help/bigChain.html +++ src/hg/htdocs/goldenPath/help/bigChain.html @@ -59,48 +59,48 @@

To create a bigChain track, follow these steps:

Step 1. If you already have a chain file you would like to convert to a bigChain, skip to Step 3. Otherwise download this example chain file for the human GRCh38 (hg38) assembly.

Step 2. Download these autoSql files needed by bedToBigBed: bigChain.as and bigLink.as.

Step 3. Download the bedToBigBed and chainToBigChain programs from the UCSC -binary utilities directory.

+binary utilities directory.

Step 4. Use the fetchChromSizes script from the -same directory to create a +same directory to create a chrom.sizes file for the UCSC database with which you are working (e.g., hg38). Alternatively, you can download the chrom.sizes file for any assembly hosted at UCSC from our -downloads page (click on "Full +downloads page (click on "Full data set" for any assembly). For example, the hg38.chrom.sizes file for the hg38 database is located at -http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes.

+http://hgdownload.gi.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes.

Here are wget commands to obtain these above files.

wget https://genome.ucsc.edu/goldenPath/help/examples/bigChain.as
 wget https://genome.ucsc.edu/goldenPath/help/examples/bigLink.as
-wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes
+wget http://hgdownload.gi.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes
 wget https://genome.ucsc.edu/goldenPath/help/examples/chr22_KI270731v1_random.hg38.mm10.rbest.chain

Step 5. Use the chainToBigChain utility to generate the pre-bigChain and pre-bigLink files:

chainToBigChain chr22_KI270731v1_random.hg38.mm10.rbest.chain bigChain.pre bigChain.link.pre

Step 6. Create the bigChain and bigLink files using the bedToBigBed utility:

bedToBigBed -type=bed6+6 -as=bigChain.as -tab bigChain.pre hg38.chrom.sizes bigChain.bb
 bedToBigBed -type=bed4+1 -as=bigLink.as -tab bigChain.link.pre hg38.chrom.sizes bigChain.link.bb

Step 7. Move the newly created bigChain (bigChain.bb) and bigLink (bigChain.link.bb) @@ -151,64 +151,64 @@ to that which is available for a standard chain track.

Example #2

In this example, you will create your own bigChain file from an existing chain input file.

Save this chain file to your computer (Step 1 in Creating a bigChain track, above).
Save the autoSql files bigChain.as and bigLink.as to your computer (Step 2, above).
Download the bedToBigBed and chainToBigChain - utilities (Step 3, above).

utilities

Step 3

Save the hg38.chrom.sizes text file to your computer. This file contains the chrom.sizes for the human hg38 assembly (Step 4, above).
Run the utilities in Steps 5-7, above, to create the bigChain and bigLink output files.
Place the newly created bigChain (bigChain.bb) and and bigLink (bigChain.link.bb) files on a web-accessible server (Step 8).
Construct a track line that points to the bigChain file (Step 9, above).
Create the custom track on the human assembly hg38 (Dec. 2013), and view it in the Genome Browser (Step 10, above).

Sharing your data with others

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

Extracting data from the bigChain format

Because the bigChain 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.