src/utils/userApps/bigBedWigs.txt 1.2

Index: src/utils/userApps/bigBedWigs.txt
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RCS file: /projects/compbio/cvsroot/kent/src/utils/userApps/bigBedWigs.txt,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 1000000 -r1.1 -r1.2
--- src/utils/userApps/bigBedWigs.txt	26 Mar 2009 23:15:45 -0000	1.1
+++ src/utils/userApps/bigBedWigs.txt	30 Mar 2009 17:37:01 -0000	1.2
@@ -1,71 +1,75 @@
 
 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
+	wigToBigWig input.wig.gz chrom.sizes myBigWig.bw
+    if your input.wig.gz file has 'track' and 'browser' lines:
+	zcat input.wig.gz | egrep -v "^track|^browser" \
+	    wigToBigWig stdin 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 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
 
 
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 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
+       bedToBigBed input.bed.gz chrom.sizes myBigBed.bb
+    if your input.bed.gz file has 'track' and 'browser' lines:
+	zcat input.bed.gz | egrep -v "^track|^browser" \
+	    bedToBigBed stdin chrom.sizes myBigWig.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 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 
 
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