The bigGenePred format stores positional annotation items for collections of exons in a compressed format, similar to how BED files can be compressed into bigBeds. The bigGenePred format includes 8 additional fields that contain details about coding frames, annotation status, and other gene-specific information. This is commonly used in the Browser to display start codons, stop codons, and amino acid translations.
Before compression, bigGenePred files can be described as bed12+8 files. bigGenePred
files can be created using the program bedToBigBed, run with the -as
option to pull in a special
autoSql (.as) file that defines the extra fields of the bigGenePred.
Much like bigBed, bigGenePred files are in an indexed binary format. The advantage of using a binary format is that only the portions of the file needed to display a particular region are read by the Genome Browser server. Because of this, indexed binary files have much faster display performance than regular BED format files when working with large data sets. The bigGenePred file remains on the user's web-accessible server (http, https or ftp) and only the portion needed to display the current genome position is cached as a "sparse file". If you want more information on finding a a web-accessible server or need hosting space for your bigGenePred files, please see the Hosting section of the Track Hub Help documentation.
The following autoSql definition specifies bigGenePred gene prediction files. This
definition, contained in the file bigGenePred.as,
is pulled in when the bedToBigBed utility is run with the
-as=bigGenePred.as option.
table bigGenePred
"bigGenePred gene models"
(
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 thickStart; "Start of where display should be thick (start codon)"
uint thickEnd; "End of where display should be thick (stop codon)"
uint reserved; "RGB value (use R,G,B string in input file)"
int blockCount; "Number of blocks"
int[blockCount] blockSizes; "Comma separated list of block sizes"
int[blockCount] chromStarts;"Start positions relative to chromStart"
string name2; "Alternative/human readable name"
string cdsStartStat; "Status of CDS start annotation (none, unknown, incomplete, or complete)"
string cdsEndStat; "Status of CDS end annotation (none, unknown, incomplete, or complete)"
int[blockCount] exonFrames; "Exon frame {0,1,2}, or -1 if no frame for exon"
string type; "Transcript type"
string geneName; "Primary identifier for gene"
string geneName2; "Alternative/human-readable gene name"
string geneType; "Gene type"
) The following bed12+8 is an example of a bigGenePred input file .
To create a bigGenePred track, follow these steps:
Step 1.
Format your bigGenePred file. The first 12 fields of the bigGenePred bed12+8 format are described by the
basic BED file format. You can also read
the genePred format.
Your bigGenePred file must also contain the 8 extra fields described in the autoSql file definition
shown above: name2, cdsStartStat, cdsEndStat, exonFrames, type, geneName, geneName2,
geneType. For reference, you can use this example bed12+8 input file,
bigGenePred.txt. Your bigGenePred file must be sorted
first on the chrom field, and secondarily on the chromStart field. You
can use the UNIX sort command to do this:
sort -k1,1 -k2,2n unsorted.bed > input.bed
Step 2.
Download the bedToBigBed program from the
binary utilities directory.
Step 3.
Download the chrom.sizes file for your genome assembly using the fetchChromSizes
script from the same directory.
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, the hg38.chrom.sizes file for the hg38
database is located at
http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes.
Step 4.
Create the bigGenePred file from your sorted input file using the bedToBigBed
utility command:
bedToBigBed -as=bigGenePred.as -type=bed12+8 bigGenePred.txt chrom.sizes myBigGenePred.bbStep 5. Move the newly created bigGenePred file (myBigGenePred.bb) to a web-accessible http, https, or ftp location. See hosting section if necessary.
Step 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 basic version of the track line will look something like this:
track type=bigGenePred name="My Big GenePred" description="A Gene Set Built from Data from My Lab" bigDataUrl=http://myorg.edu/mylab/myBigGenePred.bbStep 7. Paste this custom track line into the text box on the custom track management page.
The bedToBigBed program can be run with several additional options. For a full list of
the available options, type bedToBigBed (with no arguments) on the command line to
display the usage message.
In this example, you will create a bigGenePred custom track using a bigGenePred file located on the UCSC Genome Browser http server, bigGenePred.bb. This file contains data for the hg38 assembly.
To create a custom track using this bigGenePred file:
track type=bigGenePred name="bigGenePred Example One" description="A bigGenePred file" bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigGenePred.bbCustom tracks can also be loaded via one URL line. The link below loads the same bigGenePred track and sets additional parameters in the URL:
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hgct_customText=track%20type=bigGenePred%20bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigGenePred.bbAfter this example bigGenePred track is loaded in the Genome Browser, click on a gene in the browser's track display to view the details page for that gene. Note that the page offers links to several sequence types, including translated protein, predicted mRNA, and genomic sequence.
In this example, you will configure the bigGenePred track loaded in Example #1 to display codons and amino acid numbering:
chr9:133,255,650-133,255,700, and note that the track now displays codons.
You can also add a parameter in the custom track line, baseColorDefault=genomicCodons,
to set display codons by default:
browser position chr10:67,884,600-67,884,900
track type=bigGenePred baseColorDefault=genomicCodons name="bigGenePred Example Two" description="A bigGenePred file" visibility=pack bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigGenePred.bb Paste the above into the hg38 custom track management page to view an example of bigGenePred amino acid display at the beginning of the SIRT1 gene on chromosome 10.
In this example, you will create your own bigGenePred file from an existing bigGenePred input file.
bedToBigBed
utility (Step 2, in the Creating a bigGenePred section above).bedToBigBed utility to create the bigGenePred output file (step 4,
above):
bedToBigBed -type=bed12+8 -tab -as=bigGenePred.as bigGenePred.txt hg38.chrom.sizes bigGenePred.bbIn this example, you will convert a genePred file to bigGenePred using command line utilities. +
In this example, you will convert a GTF file to bigGenePred using command line utilities. You can download utilities from the utilities directory.
wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/wgEncodeGencodeCompV28.txt.gzwget http://genome.ucsc.edu/goldenPath/help/examples/bigGenePredExample4.gtfgunzip wgEncodeGencodeCompV28.txt.gz gtfToGenePred -genePredExt bigGenePredExample4.gtf example4.genePredcut -f 2- wgEncodeGencodeCompV28.txt > wgCompV28Cut.txt genePredToBigGenePred example4.genePred ex4BigGenePred.txtgenePredToBigGenePred wgCompV28Cut.txt wgEncodeGencodeCompV28BigGP.txtfetchChromSizes hg38 > hg38.chrom.sizes
-wget https://hgwdev.gi.ucsc.edu/goldenPath/help/examples/bigGenePred.asbedToBigBed -type=bed12+8 -tab -as=bigGenePred.as wgEncodeGencodeCompV28BigGP.txt hg38.chrom.sizes wgEncodeGencodeCompV28.bgpbedToBigBed -type=bed12+8 -tab -as=bigGenePred.as ex4BigGenePred.txt hg38.chrom.sizes ex4BigGenePred.bbhttp://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hgct_customText=track%20type=bigGenePred%20bigDataUrl=https://hgwdev.gi.ucsc.edu/~dschmelt/wgEncodeGencodeCompV28.bgphttp://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hgct_customText=track%20type=bigGenePred%20bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/ex4bigGenePred.bbbaseColorDefault=genomicCodons code as is done below.
+desciption. If you want to see codons, you can right click, then click configure codon view or
+set these options using the baseColorDefault=genomicCodons code as is done below.
browser position chr10:67,884,600-67,884,900
-track type=bigGenePred baseColorDefault=genomicCodons name="bigGenePred Example Four" description="BGP Made from genePred" visibility=pack bigDataUrl=https://hgwdev.gi.ucsc.edu/~dschmelt/wgEncodeGencodeCompV28.bgpIf you would like to share your bigGenePred data track with a colleague, learn how to create a URL link to your data by looking at Example #6.
Because the bigGenePred 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.
-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.
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
row(s) before running the bedToBigBed program.