Submitting Tracks for the Genome Browser
The UCSC Genome Browser requires data be submitted in a certain format and with a specific process. (The Hub is working with UCSC to create output that is more tailored to the needs of the FaceBase community.) The following are highlights of the steps you need to take. For more detailed information, see the UCSC page on TBD.
Format the data
The data tracks provided by a hub must be formatted in one of the compressed binary index formats supported by the Genome Browser: bigWig, bigBed, BAM or VCF.
- The bigWig format is best for displaying continuous value plot data, such as read depths from short read sequencing projects or levels of conservation observed in a multiple-species alignment. A bigWig file contains a list of chromosome segments, each of which is associated with a floating point value. When graphed, the segments may appear as a big "wiggle". Although each bigWig file can contain only a single value for any given base, bigWig tracks are often combined into "container multiWig" or "compositeTrack on" tagged tracks. For information on creating and configuring bigWig tracks, see the bigWig Track Format help page.
- BigBed files are binary indexed versions of Browser Extensible Data (BED) files. BED format is useful for associating a name and (optionally) a color and a score with one or more related regions on the same chromosome, such as all the exons of a gene. See the bigBed Track Format help page for information on creating and configuring bigBed tracks.
- BAM files contain alignments of (generally short) DNA reads to a reference sequence, usually a complete genome. BAM files are binary versions of Sequence Alignment/Map (SAM) format files. Unlike bigWig and bigBed formats, the index for a BAM file is in a separate file, which the track hub expects to be in the same directory with the same root name as the BAM file with the addition of a .bai suffix. See the BAM Track Format help page for more information.
- VCF (Variant Call Format) files can contain annotations of single nucleotide variants, insertions/deletions, copy number variants, structural variants and other types of genomic variation. When a VCF file is compressed and indexed using tabix (available here), it can be used as a data track file. Unlike bigWig and bigBed formats, the tabix index is in a separate file, which the track hub expects to be in the same directory with the same root name as the VCF file with the addition of a .tbi suffix. See the VCF Track Format help page for more information.
Create the trackDb.txt files
The trackDb.txt file, which is based on the Genome Browser
.ra format, is the most complicated of the text files in the hub directory. It contains a stanza for each of the data files for the given assembly that defines display and configuration properties for the track. If the tracks are grouped into larger entities, such as composite or super-tracks, the larger entities will have a stanza in the file as well.
The Track Database Definition Document will help you understand how to create a trackDb.txt file. It goes into great detail about how to declare dataset display settings and values.
At a minimum, each trackDb.txt file must contain at least five tags:
track track_name bigDataUrl track_data_URL shortLabel short_label longLabel long_label type track_type
- The symbolic name of the track. The first character must be a letter, and the remaining characters must be letters, numbers, or underscore (
_). Each track must have a unique name. This tag pair must be the first entry in the trackDb.txt file.
- The file name, path, or Web location of the track's data file. The bigDataUrl can be a full URL. If it is not prefaced by a protocol, such as
ftp://, then it is considered to be a path relative to the trackDb.txt file.
- The short name for the track displayed in the track list, in the configuration and track settings, and on the details pages. Suggested maximum length is 17 characters.
- The longer description label for the track that is displayed in the configuration and track settings, and on the details pages. Suggested maximum length is 80 characters.
- The format of the file specified by bigDataUrl. Must be either bigWig, bigBed, bam or vcfTabix. If the type is bigBed, it may be followed by an optional number denoting the number of fields in the bigBed file (e.g., "type bigBed 12" for a file with 12 fields). If no number is given, a default value of 3 is assumed (a very limited display that omits names, strand information, and exon boundaries).
Example 4: Sample trackDb.txt file containing two simple tracks
track dnaseSignal bigDataUrl dnaseSignal.bigWig shortLabel DNAse Signal longLabel Depth of alignments of DNAse reads type bigWig track dnaseReads bigDataUrl dnaseReads.bam shortLabel DNAse Reads longLabel DNAse reads mapped with MAQ type bam
Default subtracks for composite
For each composite, it is recommended that a subset of subtracks are 'selected' (on) by default. This way, when a user turns the composite from hide to another visibility, they will see tracks displayed in the browser.
Default composites within a super-track
For super-tracks that you don't want displaying by default when your track hub is turned on, it is recommended that some (or all) composites within the super-track be set to dense (or some visibility other than hide) by default and that the super-track be set to hide by default. This way, if a user changes a super-track from hide to show from the controls under the browser image, tracks are displayed. To implement, change the visibility line in trackDb of the super-tracks to hide and the visibility lines of all or some of the composite tracks within to dense (or some visibility other than hide).
In addition to the controls for each view (click on the title of the view drop-down), there is often another set of controls above the view drop-downs (just under the 'Overall display mode'). This set of controls is not associated with a particular view and clashes with the view controls. It is recommended to remove the controls that are not associated with a particular view.