track bigBed1
bigDataUrl searchFile3.bb
shortLabel bigBed example
longLabel 
type bigBed
visibility dense
searchIndex name
searchTrix outFile3.ix
html ../trackInfo


#To obtain the original bigBed file use the following command: rsync -Ap rsync://hgdownload.soe.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCaltechRnaSeq/wgEncodeCaltechRnaSeqGm12891R2x75Il200JunctionsRep1V3.bigBed ./file3.bb
# rsync file, expand to bed with bigBedToBed, bigBedToBed file3.bb file3.bed, use top of original.bb to get .as definitions, make changes as desired, and call file3.as
# note file3.as needs tab deliniations after the semi-colon, such as name;-tab-"Name of item", if you cut and paste from the head of file3.bb, you need to clean it up.
# use the file3.as and run bedToBigBed -as=file3.as -type=bed6+3 -extraIndex=name file3.bed hg19.chrom.sizes searchFile3.bb
# add "searchIndex name" and will now be able to search for items in name like SJ_96833_AA|GG


#To create a further search on text describing items such as SJ_96833_AA|GG, you create a second file, (in this case by using original file3.bed)
#You can chop off the coordinates on file3.bed and send the data to a text file called infoSJs.txt,   cat file3.bed | sed -e 's/^.*SJ/SJ/' > infoSJs.txt
#The general format for these text files is "id  text about id\n id2 text about id2\n" see infoSJs.txt
#You can use the ixIxx program to create a trix file: ixIxx infoSJs.txt outFile3.ix outFile3.ixx
#Learn more at these links: http://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html#searchTrix  and http://genome.ucsc.edu/goldenPath/help/trix.html
#You can then add the line "searchTrix outFile3.ix" to the trackDb.txt and you will be able to search on the infoSJs.txt fields.
#For example a infoSJs.txt line like "SJ_96833_AA|GG          996    +           2053    -1   996", can now be searched and found by just looking up 2053 

#Also see these archived mailing list questions for further information:
#https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/1ZWq30-89fw/R_Wdc0Z1-X4J
#https://groups.google.com/a/soe.ucsc.edu/forum/#!msg/genome/x26OjYKCRAo/soImKyEZrt8J