bigChain Track Format
 

The bigChain format describes a pairwise alignment that allow gaps in both sequences simultaneously. bigChain files are Chain files compressed and indexed as a bigBed.

bigChain files are created using the program bedToBigBed with a special AutoSQL file that defines the fields of the bigChain. The resulting bigBed files are in an indexed binary format. The main advantage of the bigBed files is that only portions of the files needed to display a particular region are transferred to UCSC. So for large data sets, bigBed is considerably faster than regular BED files. The bigBed file remains on your web accessible server (http, https, or ftp), not on the UCSC server. Only the portion that is needed for the chromosomal position you are currently viewing is locally cached as a "sparse file".

Big Gene Predictions

The following AutoSQL definition is used for bigChain gene prediction files. This is the bigChain.as file defined by the -as= option when using bedToBigBed. Click this bed6+6 file for an example of bigChain input.
table bigChain
"bigChain pairwise alignment"
    (
    string chrom;       "Reference sequence chromosome or scaffold"
    uint   chromStart;  "Start position in chromosome"
    uint   chromEnd;    "End position in chromosome"
    string name;        "Name or ID of item, ideally both human readable and unique"
    uint score;         "Score (0-1000)"
    char[1] strand;     "+ or - for strand"
    uint tSize;         "size of target sequence"
    string qName;       "name of query sequence"
    uint qSize;         "size of query sequence"
    uint qStart;        "start of alignment on query sequence"
    uint qEnd;          "end of alignment on query sequence"
    uint chainScore;    "score from chain"
    )

Note that the bedToBigBed utility uses a substantial amount of memory; somewhere on the order of 1.25 times more RAM than the uncompressed BED input file.

To create a bigChain track, follow these steps:

this commands need to be included in the below text

hgLoadChain -noBin -test hg38 bigChain chr22_KI270731v1_random.hg38.mm10.rbest.chain
 sed 's/.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7,$9,$10,$1}' > chr22_KI270731v1_random.hg38.mm10.rbest.bigChain
bedToBigBed -type=bed6+5 -tab -as=bigChain.as chr22_KI270731v1_random.hg38.mm10.rbest.bigChain chrom.sizes bigChain.bb
 awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n  > bigChain.bigLink
  bedToBigBed -type=bed4+1 -as=bigLink.as bigChain.bigLink chrom.sizes bigChain.link.bb
  1. Create a bed6+6 bigChain format file that has the first twelve fields described by a normal BED file as described here. (You can also read about genePred here.)
    • Your bigChain file must have the extra eight fields described in the AutoSQL file above: name2, cdsStartStat, cdsEndStat, exonFrames, type, geneName, geneName2, geneType.
    • Your bigChain file must be sorted by chrom then chromStart. You can use the UNIX sort command to do this: sort -k1,1 -k2,2n unsorted.bed > input.bed
  2. Download the bedToBigBed program from the directory of binary utilities.
  3. Use the fetchChromSizes script from the same directory to create a chrom.sizes file for the UCSC database you are working with (e.g. hg38). Alternatively, you can download the chrom.sizes file for any assembly hosted at UCSC from our downloads page (click on "Full data set" for any assembly). For example, for the hg38 database, the hg38.chrom.sizes are located at http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes.
  4. Create the bigBed file from your sorted bigChain input file using the bedToBigBed utility like so: bedToBigBed -as=bigChain.as -type=bed12+8 bigChain.txt chrom.sizes myBigGenePred.bb
  5. Move the newly created bigBed file (myBigGenePred.bb) to an http, https, or ftp location.
  6. Construct a custom track using a single track line. Note that any of the track attributes listed here are applicable to tracks of type bigBed. The most basic version of the "track" line will look something like this:
    track type=bigChain name="My Big Chain" bigDataUrl=http://myorg.edu/mylab/myBigGenePred.bb linkDataUrl=http://myorg.edu/mylab/myBigGenePred.bb
  7. Paste this custom track line into the text box in the custom track management page.
The bedToBigBed program can also be run with several additional options. A full list of the available options can be seen by running bedToBigBed with no arguments to display the usage message.

Example One

In this example, you will use an existing bigChain file to create a bigChain custom track. A bigChain file that contains data on the hg38 assembly has been placed on our http server. You can create a custom track using this bigChain file by constructing a "track" line that references this file like so:

track type=bigChain name="bigChain Example One" description="A bigChain file" bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigChain.bb

Paste the above "track" line into the custom track management page for the human assembly hg38 (Dec. 2013), then press the submit button.

Custom tracks can also be loaded via one URL line. The below link loads the same bigChain track, but includes parameters on the URL line:

http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hgct_customText=track%20type=bigChain%20name=Example%20bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigChain.bb

With this example bigChain loaded, click into a gene from the track. Note that the details page has a "Links to sequence:" section that includes "Translated Protein", "Predicted mRNA", and "Genomic Sequence" links. Click the "Go to ... track controls" link. There change the "Color track by codons:" option from "OFF" too "genomic codons" and be sure "Display mode:" is "full" then click "Submit". Then zoom to a region where amino acids display, such as chr9:133,255,650-133,255,700 and see how bigChain allows the display of codons. Click back into the track controls page and click the box next to "Show codon numbering". Return to the browser to see amino acid numbering.

You can also add a parameter in the custom track line, baseColorDefault=genomicCodons, to set the display of codons:

browser position chr10:67,884,600-67,884,900
track type=bigChain baseColorDefault=genomicCodons name="bigChain Example Two" description="A bigChain file" visibility=pack bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigChain.bb

Paste the above into the hg38 custom track page to see an example of bigChain amino acid display around the beginning of the gene SIRT1 on chromosome 10.

Example Two

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

  • Save this bed12+8 bigChain.txt example input file to your machine (satisfies above step 1).
  • Download the bedToBigBed utility (step 2).
  • Save this hg38.chrom.sizes text file to your machine. It contains the chrom.sizes for the human (hg38) assembly (step 3).
  • Save this bigChain.as text file to your machine.
  • Run the utility to create the bigBed output file (step 4):
    bedToBigBed -type=bed12+8 -tab -as=bigChain.as bigChain.txt hg38.chrom.sizes bigChain.bb
  • Place the bigBed file you just created (bigChain.bb) on a web-accessible server (step 5).
  • Construct a "track" line that points to your bigChain file (see step 6).
  • Create the custom track on the human assembly hg38 (Dec. 2013), and view it in the genome browser (see step 7).
Note the above description in Example One on how to view genomic codons, including numbering.

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 11 on this page.

Extracting Data from bigBed Format

Since the bigChain files are an extension of bigBed files, which are indexed binary files, they can be difficult to extract data from. We have developed the following programs, all of which are available from the directory of binary utilities.

  • bigBedToBed — this program converts a bigBed file to ASCII BED format.
  • bigBedSummary — this program extracts summary information from a bigBed file.
  • bigBedInfo — this program prints out information about a bigBed file.
As with all UCSC Genome Browser programs, simply type the program name at the command line with no parameters to see the usage statement.

Troubleshooting

If you encounter an error when you run the bedToBigBed program, it may be because your input bigChain file has data off the end of a chromosome. In this case, use the bedClip program here before the bedToBigBed program. It will remove the row(s) in your input BED file that are off the end of a chromosome.