The Genome Browser supports searching for items within bigBed tracks in track data hubs. To support this behavior you have to add an index to the bigBed file when you initially create the the bigBed file from the bed file input. Indices are usually created on the name field of the bed, but can be created on any field of the bed. Free-text searches can also be enabled by creating a TRIX index file that maps id's in the track to free-text metadata. Further instructions can be found in the Searchable Hub Quick Start Guide.
See the searchIndex and searchTrix fields in the Hub Track
Database Definition document for
information on how to set up your bigBed to enable searching. The searchIndex setting requires
-the input BED data to be case-senstive sorted (sort -k1,1 -k2,2n). You can use
-either the example UNIX sort command or the bedSort utility available
-here. See an example
-searchable hub.
sort -k1,1 -k2,2n), which can be done
+using the -sort option in the bedToBigBed utility.
+
+When a bigBed file is used in a track hub, additional indices can be created to support searching
+on specific fields. For example, running bedToBigBed with -extraIndex=name
+builds an index on the name field. You can then enable searching on that field by adding:
searchIndex nameto the stanza for that bigBed track in the hub's trackDb.txt file. See the +searchable hub example.
The Genome Browser supports three varieties of data filter options for bigBed data. These can improve data usability in many ways, such as displaying specific data by default (e.g. only items that pass certain quality scores), allow for filtering based on pre-specified categories (e.g designate only LINE repetitive elements from a list of options) and more.
For more information on the options available and examples on how to set up filters, see our Track Hub Filters Quick Start Guide and the filter entries in the Track Database Definition Document.