bigMaf Track Format

The bigMaf format stores multiple alignments in a format compatible with MAF files, which are then compressed and indexed as bigBeds. bigMaf files are created using the program bedToBigBed with a special AutoSQL file that defines the fields of the bigMaf. The resulting bigMaf files are in an indexed binary format. The main advantage of the bigMaf files is that only portions of the files needed to display a particular region are transferred to UCSC. So for large data sets, bigMaf is considerably faster than regular MAF files. The bigMaf 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 MAF

The following AutoSQL definition is used for bigMaf multiple alignment files. This is the bigMaf.as file defined by the -as option when using bedToBigBed.

table bedMaf
"Bed3 with MAF block"
    (
    string chrom;      "Reference sequence chromosome or scaffold"
    uint   chromStart; "Start position in chromosome"
    uint   chromEnd;   "End position in chromosome"
    lstring mafBlock;  "MAF block"
    ) 

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 bigMaf track, follow these steps:

  1. If you already have a MAF file you would like to convert to a bigMaf, skip to Step 3; otherwise, download the example MAF file for the Human GRCh38(hg38) assembly.
    • If you would like to include optional reading frame and block summary information with our example MAF file, please download the chr22_KI270731v1_random.gp GenePred file.
  2. Download the AutoSQL files needed by bedToBigBed:
    • bigMaf.as
    • If you would like to include optional frame summary and information with your bigMaf file, you will also want to download the mafSummary.as and mafFrames.as files.
  3. Download the bedToBigBed and mafToBigBed programs from the directory of binary utilities.
    • If you would like to generate the optional frame and summary files for your multiple alignment, also download the hgLoadMafSummary, genePredSingleCover, and genePredToMafFrames programs from the same directory.
  4. 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.
    mafToBigMaf hg38 chr22_KI270731v1_random.maf stdout | sort -k1,1 -k2,2n > bigMaf.txt
    bedToBigBed -type=bed3+1 -as=bigMaf.as -tab bigMaf.txt hg38.chrom.sizes bigMaf.bb 
  5. Follow the below steps to create the binary indexed mafFrames and mafSummary files to accompany your bigMaf file:
    genePredSingleCover chr22_KI270731v1_random.gp single.gp
    genePredToMafFrames hg38 chr22_KI270731v1_random.maf bigMafFrames.txt hg38 single.gp
    bedToBigBed -type=bed3+8 -as=mafFrames.as -tab bigMafFrames.txt hg38.chrom.sizes bigMafFrames.bb
    
    hgLoadMafSummary -minSeqSize=1 -test hg38 bigMafSummary chr22_KI270731v1_random.maf
    cut -f 2 bigMafSummary.tab | sort -k1,1 -k2,2n > bigMafSummary.bed
    bedToBigBed -type=bed3+4 -as=mafSummary.as -tab bigMafSummary.bed hg38.chrom.sizes bigMafSummary.bb 
  6. Move the newly created bigMaf file (bigMaf.bb) to an http, https, or ftp location.
    • If you generated the bigMafSummary.bb and/or bigMafFrames.bb files, they will also need to be in a web accessible location, likely in the same location as bigMaf.bb.
  7. 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=bigMaf name="My Big MAF" description="A Multiple Alignment"
    bigDataUrl=http://myorg.edu/mylab/bigMaf.bb
  8. Paste this custom track line into the text box on the custom track management page.

The bedToBigBed program can also be run with several additional options. Run bedToBigBed with no arguments to view a full list of available options.

Example #1

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

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

Paste the above "track" line into the custom track management page for the human assembly hg38 (Dec. 2013), then press the submit button. Please note that additional track line options exist that are specific for the MAF format. For instance, adding speciesOrder="panTro4 rheMac3 mm10 rn5 canFam3 monDom5" to the above example will allow specifying the order of sequences.

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

http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chr22_KI270731v1_random&hgct_customText=track%20type=bigMaf%20name=Example%20bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigMaf.bb%20visibility=pack

With this example bigMaf loaded, click into an alignment from the track. Note that the details page has information about the individual alignments, similar to the details page of a standard MAF track.

Example #2

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

Sharing your data with others

If you would like to share your bigMaf data track with a colleague, learn how to create a URL by looking at Example 11 on this page.

Extracting data from the bigMaf format

Since the bigMaf 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.

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 bigMaf 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.