yAxisNumLabels.<on/off> <integer>bigDataUrl <url/relativePath>Required: For Hubs
The location of a remote data file containing the bulk of the data for the track. This setting is required for all data tracks in a track hub.
The setting is either the full URL (including http: or another protocol)
or it is relative to the directory in which the trackDb file containing this setting
is located. The file must be in one of
the supported remote data file formats: bam/cram, bigBarChart, bigBed, bigChain, bigLolly,
- bigInteract, bigMaf, bigPsl, bigGenePred, bigNarrowPeak, bigWig, vcfTabix, or hic.
+ bigInteract, bigMaf, bigPsl, bigGenePred, bigMethyl, bigNarrowPeak, bigWig, vcfTabix, or hic.
Note that bam/cram and vcfTabix/vcfPhasedTrio types require a separate
index file that must have the same name as the data file plus a
standard suffix (".bai" and ".tbi" respectively), unless bigDataIndex is used.
All occurrences of the string $D in the URL will be
substituted with the genome assembly database name. This allows a
trackDb entry to be used with for multiple assemblies. $D
substitution is not implemented for track hubs.
Example:
bigDataUrl http://vizhub.wustl.edu/VizHub/hg19/biBrainH3K4me1.bbor
bigDataUrl biBrainH3K4me1.bb
If an entry of comma-separated values contains a "|" symbol, the part before the pipe symbol is used to replace the $$ wildcard and the part after it is used as the label, as opposed to the default label description in the .as file. This pipe substitution is similar to how Wikipedia markup encodes links. In the example below, a value for the field pmid of "11932250|W James Kent" would create a link with the URL https://www.ncbi.nlm.nih.gov/pubmed/11932250 and the label "W James Kent".
Example:
urls pmid="https://www.ncbi.nlm.nih.gov/pubmed/$$" spId="http://www.uniprot.org/uniprot/$$"
-skipEmptyFields onIf this setting is "on", the item details page will not show fields that have empty values. This can be useful when you have numerous extra fields but only few of them have a value.
skipFields <fieldName1>="<url1>" <fieldName2>="<url2>" ...This setting can be used to suppress extra fields on the item details page. It can be useful if you do not want to show fields that are only used for mouseOvers or labels.
Example:
skipFields mouseOver,labelField,hiddenField
sepFields fieldName1,fieldName2 ...This setting changes the item details page and splits the table used for showing extra fields before any of the specified fields. It can be useful to visually separate extra fields into logical categories.
Example:
sepFields pmid,spId
mouseOverField <fieldName1>For bigBed files with more than 8 fields (not counting any extra bigBed fields), this adds mouse over text that are different from the "name" field of a bigBed file. If the field is empty then the mouse over will fallback to the name field.
To make this work, create a bigBed file with at least 8 columns and put the text for the mouse over into an extra bigBed field as explained in example 3 of the bigBed documentation. The field name from your .as file is the field name for this statement.
Example:
mouseOverField comment
mouseOver <pattern>For bigBed files with more than 8 fields (not counting any extra bigBed fields), this adds mouse over text from a pattern based on the values of fields in the file. The pattern is constructed with fieldnames from the .as file, preceded by the dollar sign ($) and optional curly braces ({}), and can include arbitrary text between the field names. When field names may be prefixes or overlap with one another, as in the below example, curly braces can be used to more clearly define the field name to be used.
Example:
mouseOver variant $name/$chrom:${chromStart} value $score
@@ -1091,30 +1091,40 @@
The bigPsl format stores alignments between two sequences, as PSL files do, but they are compressed and indexed as bigBeds. bigPsl files are created using the program bedToBigBed with a special AutoSQL file that defines the fields of the bigPsl. The resulting bigPsl files are in an indexed binary format. The main advantage of the bigPsl files is that only portions of the files needed to display a particular region are transferred to UCSC. So for large data sets, bigPsl is considerably faster than regular PSL files. The bigPsl 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".
For complete bigPsl format definitions please see the
bigPsl help page.
The bigGenePred format stores annotation items that are a linked collection of exons, much as BED files indexed as bigBeds do, but bigGenePred has additional information about the coding frames and other gene specific information in eight additional fields. bigGenePred files are created using the program bedToBigBed with a special AutoSQL file that defines the fields of the bigGenePred. 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". For complete bigGenePred format definitions please see the bigGenePred help page.
+ The bigMethyl format stores methylation sights. bigMethyl files are based on the bigBed format. The first nine fields are the same as bed. The other nine include various scores. + + bigMethyl files are created using the program bedToBigBed with a special AutoSQL file that defines the fields of the bigMethyl. 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". + For complete bigMethyl format definitions please see the + bigMethyl help page.
+The bigNarrowPeak format stores peaks over a range with a single basepair central peak. bigNarrowPeak files are based on the bigBed format. The first six fields are the same as bed. The other four include three scores, and the base-pair offset of the central peak. bigNarrowPeak files are created using the program bedToBigBed with a special AutoSQL file that defines the fields of the bigNarrowPeak. 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". For complete bigNarrowPeak format definitions please see the bigNarrowPeak help page.
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". For complete bigMaf format definitions please see the