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bigNarrowPeak is a format used to provide called peaks of signal enrichment based on pooled, normalized (interpreted) data. The bigNarrowPeak format stores annotation items that are a single block with a single base peak within that block, much as BED files indexed as bigBeds do. A bigNarrowPeak file is a standard six field bed with four additional fields (BED6+4 format) that contain three doubles with scoring information and the location of the single base peak. It is the binary version of the ENCODE narrowPeak or point-source peak format.
The bigNarrowPeak files are 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 bigNarrowPeak.
The bigNarrowPeak files are in an indexed binary format. The main advantage of this format is that only those portions of the file needed to display a particular region are transferred to the Genome Browser server. Because of this, indexed binary files have considerably faster display performance than regular BED format files when working with large data sets. The bigNarrowPeak file remains on your local web-accessible server (http, https or ftp), not on the UCSC server, and only the portion needed for the currently displayed chromosomal position is locally cached as a "sparse file". If you do not have access to a web-accessible server and need hosting space for your bigNarrowPeak files, please see the Hosting section of the Track Hub Help documentation.
The following autoSql definition is used to specify bigNarrowPeak files. This
definition, contained in the file bigNarrowPeak.as,
is pulled in when the
bedToBigBed utility is run with the
table bigNarrowPeak "BED6+4 Peaks of signal enrichment based on pooled, normalized (interpreted) data." ( string chrom; "Reference sequence chromosome or scaffold" uint chromStart; "Start position in chromosome" uint chromEnd; "End position in chromosome" string name; "Name given to a region (preferably unique). Use . if no name is assigned" uint score; "Indicates how dark the peak will be displayed in the browser (0-1000) " char strand; "+ or - or . for unknown" float signalValue; "Measurement of average enrichment for the region" float pValue; "Statistical significance of signal value (-log10). Set to -1 if not used." float qValue; "Statistical significance with multiple-test correction applied (FDR -log10). Set to -1 if not used." int peak; "Point-source called for this peak; 0-based offset from chromStart. Set to -1 if no point-source called." )
Click here to view an example of a bigNarrowPeak (bed6+4) input file.
Note that the
bedToBigBed utility uses a substantial amount of memory: approximately
25% more RAM than the uncompressed BED input file.
To create a bigNarrowPeak track, follow these steps:
Create a bigNarrowPeak file. The first six fields of the bigNarrowPeak bed6+4 format are
described by the basic BED file format shown here.
You can also read about narrowPeak (or point-source peak),
the precursor to bigNarrowPeak, here.
Your bigNarrowPeak file must also contain the four extra fields described in the autoSql file definition
signalValue, pValue, qValue, peak.
Your bigNarrowPeak file must be sorted first on the
chrom field, and
secondarily on the
chromStart field. You can use the UNIX
sort command to
sort -k1,1 -k2,2n unsorted.bed > input.bed
bedToBigBed program from the
binary utilities directory.
fetchChromSizes script from the
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
data set" for any assembly). For example, the hg38.chrom.sizes file for the hg38
database is located at
Create the bigNarrowPeak file from your sorted input file using the
bedToBigBed -as=bigNarrowPeak.as -type=bed6+4 bigNarrowPeak.txt chrom.sizes myBigNarrowPeak.bb
Step 5. Move the newly created bigNarrowPeak file (myBigNarrowPeak.bb) to a web-accessible http, https, or ftp location.
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 bigNarrowPeak. The basic version of the track line will look something like this:
track type=bigNarrowPeak name="My Big NarrowPeak" description="A Set of Peaks from DNase Experiments" bigDataUrl=http://myorg.edu/mylab/myBigNarrowPeak.bb
Step 7. Paste this custom track line into the text box on the custom track management page.
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. If you do not have access to a web-accessible server and need hosting
space for your bigNarrowPeak files, please see the Hosting
section of the Track Hub Help documentation.
In this example, you will create a bigNarrowPeak custom track using a bigNarrowPeak file, bigNarrowPeak.bb, located on the UCSC Genome Browser http server. This file contains data for the hg38 assembly.
To create a custom track using this bigNarrowPeak file:
track type=bigNarrowPeak name="bigNarrowPeak Example One" description="A bigNarrowPeak file" bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigNarrowPeak.bb
Custom tracks can also be loaded via one URL line. The link below loads the same bigNarrowPeak track and sets additional parameters in the URL:
After this example bigNarrowPeak track is loaded in the Genome Browser, click on a peak in the browser's track display to view the details page for that peak.
In this example, you will create your own bigNarrowPeak file from an existing bigNarrowPeak input file.
bedToBigBedutility (Step 2, above).
bedToBigBedutility to create the bigNarrowPeak output file (step 4, above):
bedToBigBed -type=bed6+4 -tab -as=bigNarrowPeak.as bigNarrowPeak.txt hg38.chrom.sizes bigNarrowPeak.bb
In this example, you will see the additional filtering options available for the
signalValue, pValue, qValue fields in the bigNarrowPeak format.
signalFilter, pValueFilter, qValueFilterto the track line as well as setting limitations on those filters with additional
signalFilterLimits, pValueFilterLimits, qValueFilterLimitssettings.
These values are simply added to the earlier track line in pairs, such as
track type=bigNarrowPeak name="bigNarrowPeak Example Filter" description="A bigNarrowPeak file with additional Filter Settings" signalFilter=0 signalFilterLimits=0:18241 pValueFilter=2 pValueFilterLimits=0:300 qValueFilter=2 qValueFilterLimits=0:300 bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigNarrowPeak.bb
pValueFilterLimits=0:300, and can be given a set value for where the filter should start such as
These same options could also be used in a track hub using the bigNarrowPeak format. Here is an example track hub stanza:
track exBigNarrowPeakTrack type bigNarrowPeak visibility full signalFilter 0 signalFilterLimits 0:10000 pValueFilter 0 pValueFilterLimits 0:300 qValueFilter 0 qValueFilterLimits 0:300 shortLabel Ex bigNPk longLabel bigNarrowPeak Example bigDataUrl http://genome.ucsc.edu/goldenPath/help/examples/bigNarrowPeak.bb
Because the bigNarrowPeak 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.
Such tools can be used to obtain only features within a given range, for example:
bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/danRer10/transMap/V4/danRer10.refseq.transMapV4.bigPsl -chrom=chr6 -start=0 -end=1000000 stdout >
As with all UCSC Genome Browser programs, 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
(available here) to remove the problematic
row(s) before running the