BigBed files can store extra fields in addition to the predefined BED fields. In this example, you will create your own bigBed file from a fully featured existing BED file that -contains the standard BED fields up to and including the color field (field 9), plus two +contains the standard BED fields up to and including the color field called itemRgb +(field 9), plus two additional non-standard fields (two alternate names for each item in the file). +The standard BED column itemRgb contains an R,G,B color value (e.g. "255,0,0"). The resulting bigBed file will have nine standard BED columns and two additional non-standard user-defined columns. -The standard column 9 is called the itemRgb field, it contains an R,G,B color value (e.g. 255,0,0).
+If you add extra fields to your bigBed file, you must include an AutoSql format (.as) file describing the fields. In this file, all fields (standard and non-standard) are described with a short internal name and also a human-readable description. For more information on AutoSql, see Kent and Brumbaugh, 2002, as well as examples of .as files in this directory. - -
-The bedToBigBed program is run with the arguments -type=bed9+2 and also
+Then, the bedToBigBed program is run with the arguments -type=bed9+2 and also
-as=bedExample2.as to help correctly interpret all the columns in the data.
This example also demonstrates how to create an extra search index on the name field, and the first of the
extra fields to be used for track item search. The searchIndex setting requires the input BED data to be
case-sensitive sorted (sort -k1,1 -k2,2n), where newer versions of the tool bedToBigBed
(available here) are enhanced to catch
improper input.