src/utils/userApps/bigBedWigs.txt 1.1

Index: src/utils/userApps/bigBedWigs.txt
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RCS file: src/utils/userApps/bigBedWigs.txt
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+
+BIGWIG - BigWig files store continuous data that is displayed as a graph
+in the Genome Browser, much as wig files do.  BigWig files in fact are
+created initially from wig files, using the program wigToBigWig.  The
+resulting bigWig files are in an indexed binary format.  The main
+advantage of the BigWig files is that only the portions of the files
+needed to display a particular region are transfered to UCSC, so for
+large data sets BigWig is considerably faster than straight wig.  The
+steps for creating a bigWig track are:
+
+1) Download wigToBigWig from the directory of binary utilities:
+	 http://genome-test.cse.ucsc.edu/admin/exe/linux.x86_64/
+2) Use the fetchChromSizes script from this same directory to
+	fetch the chrom.sizes file for the UCSC database you are
+	working with.
+3) Create wig format files following the definitions in:
+	http://genome.ucsc.edu/goldenPath/help/wiggle.html
+4) Run the command line
+       wigToBigWig input.wig chrom.sizes myBigWig.bw
+5) Move the output bigWig file to a http, https, or ftp site.
+6) Create a custom track with just the track line.
+	This will look something like:
+       track type=bigWig name="My Big Wig" description="A Graph of Cool
+Data from My Lab" dataUrl=http://myorg.edu/mylab/myBigWig.bw
+
+   (track lines are single lines, no line breaks are allowed)
+
+7) Paste this custom track line into the text box in the
+	custom track management page:
+    http://genome-test.cse.ucsc.edu/cgi-bin/hgCustom
+
+
+========================================================================
+
+BIGBED - BigBed files store annotation items that can either be simple, or a
+linked collection of exons, much as bed files do.  BigBed files in fact are
+created initially from bed files, using the program bedToBigBed.   The
+resulting bigBed files are in an indexed binary format.  The main advantage of
+the bigBed files is that only the portions of the files needed to display a
+particular region are transfered to UCSC, so for large data sets bigBed is
+considerably faster than straight bed.  The steps for creating a bigBed track
+are:
+
+1) Download bedToBigBed from the directory of binary utilities:
+	 http://genome-test.cse.ucsc.edu/admin/exe/linux.x86_64/
+2) Use the fetchChromSizes script from this same directory to
+	fetch the chrom.sizes file for the UCSC database you are
+	working with.
+3) Create bed format files following the definitions in:
+	http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED
+4) Run the command line
+       bedToBigBed input.wig chrom.sizes myBigBed.bb
+5) Move the output bigBed file to a http, https, or ftp site.
+6) Create a custom track with just the track line.
+	This will look something like:
+       track type=bigBed name="My Big Bed" description="Cool Genome
+Annotations from My Lab" dataUrl=http://myorg.edu/mylab/myBigBed.bb
+
+   (track lines are single lines, no line breaks are allowed)
+
+7) Paste this custom track line into the text box in the
+	custom track management page:
+    http://genome-test.cse.ucsc.edu/cgi-bin/hgCustom
+
+BigBeds also can store extra columns past the predefined bed columns.  In this
+case you should include a .as (AutoSQL) format file describing the fields.
+See http://www.linuxjournal.com/article/5949 for information on AutoSQL 
+
+========================================================================
+	$Id$
+========================================================================