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
@@ -3100,31 +3100,31 @@
transformFunc LOG
logo onEnables
dynseq display, which graphs the signal as reference base nucleotide letters
with their heights equal to the
signal value within the bigWig track. If not sufficiently zoomed in, the bigWig will
revert to bars instead of letters by default. See a working example of the logo
dynseq display on the bigWig help page.
Example:
logo on
logoMaf <url/relativePath>The argument to logoMaf is the path to a MAF alignment (either a table or bigMaf). If set and zoomed into base level, the wiggle will be drawn as a sequence logo calculated by counting the number of each nucleotide aligned to that base, which will be scaled by the value in the wiggle.
Example:
logoMaf https://hgdownload.gi.ucsc.edu/goldenPath/hg38/multiz470way/multiz470way.bigMaf
mouseOverFunction <noAverage>Limit mouse over value display to only display the fundamental values without any averaging of multiple data points. Display will show "zoom in to see values" when fundamental individual values can not be shown. Useful for tracks where averaging values together is not a @@ -3632,31 +3632,31 @@ bamColorMode off
No special coloring will be applied to items.
bamSkipPrintQualScore .Any bam tag can be displayed on the details page by clicking on it in the Browser image. The details include quality scores by default. If these scores are not relevant for this particular bam, they may be excluded from the details page with this setting.
Example:
bamSkipPrintQualScore .
indelDoubleInsert <off/on>indelQueryInsert <off/on>indelPolyA <off/on>Insertion and deletion differences between tag sequences and the reference genome can be highlighted with the use of these settings. These options may be set by the user.
indelDoubleInsert: Use to highlight alignment gaps in both the target
(reference) and query (tag) sequence with double (=) lines.indelQueryInsert: Use to highlight an insert in the query
sequence only by drawing an orange (|)
or purple (|) vertical line.
Orange lines show unalignable regions in the middle of a sequence,
@@ -5494,31 +5494,31 @@
motifTable <table>
A bed 6 table that holds motif regions
to highlight within factorSource items.
motifMapTable <table> If motif names differ from or are not unique for factorSource item names
in the motifTable, this table can used to remap the names.
This table has a simple 2 column format: char(255) factor, char(255) motif.
motifPwmTable <table>When viewing the details of a factorSource track item containing
a binding motif in the motifTable, the
consensus motif sequence and sequence logo image can be displayed.
This setting names the table holding the position weight matrices
that provide this information.
motifMaxWindow <integer>Display of highlighted motifs in a factorSource track can be limited using this setting. In large genomic regions motifs are not well distinguished in the display, and performance is improved by suppressing the feature.
The bigBarChart format stores values of a set of variables for each genomic region in the file. BigBarChart files are created using the program bedToBigBed with a special AutoSQL file that defines the fields. The resulting files are in an indexed binary format that supports efficient remote access, so the file can be hosted on your web accessible server and displayed at UCSC. For the complete bigBarChart format definitions please see the bigBarChart help page.