src/hg/makeDb/doc/sacCer1.txt 1.8
1.8 2009/04/04 23:52:48 markd
added UW footprint tracks to sacCer1
Index: src/hg/makeDb/doc/sacCer1.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/sacCer1.txt,v
retrieving revision 1.7
retrieving revision 1.8
diff -b -B -U 4 -r1.7 -r1.8
--- src/hg/makeDb/doc/sacCer1.txt 10 Feb 2009 20:26:33 -0000 1.7
+++ src/hg/makeDb/doc/sacCer1.txt 4 Apr 2009 23:52:48 -0000 1.8
@@ -1427,4 +1427,33 @@
sacCer1 sacCer2 > do.log 2>&1
# real 3m21.840s
#############################################################################
+# uwFootprints: (2009-03-11 markd)
+# obtained from Nobel lab
+# William Stafford Noble <noble@gs.washington.edu>
+# Xiaoyu Chen <xchen@cs.washington.edu>
+
+ mkdir /hive/data/genomes/sacCer1/bed/uwFootprints
+ cd /hive/data/genomes/sacCer1/bed/uwFootprints
+
+
+ wget http://noble.gs.washington.edu/proj/footprinting/yeast.dnaseI.tagCounts.wig
+ wget http://noble.gs.washington.edu/proj/footprinting/yeast.mappability.bed
+ wget http://noble.gs.washington.edu/proj/footprinting/yeast.footprints.bed
+ chmod a-w yeast.*
+
+ wigEncode yeast.dnaseI.tagCounts.wig uwFootprintsTagCounts.wig uwFootprintsTagCounts.wib
+ # Converted yeast.dnaseI.tagCounts.wig, upper limit 13798.00, lower limit 1.00
+
+ ln -sf /hive/data/genomes/sacCer1/bed/uwFootprints/uwFootprintsTagCounts.wib /gbdb/sacCer1/wib
+ hgLoadWiggle -tmpDir=/data/tmp sacCer1 uwFootprintsTagCounts uwFootprintsTagCounts.wig
+
+ hgLoadBed -tab -tmpDir=/data/tmp sacCer1 uwFootprintsMappability yeast.mappability.bed
+ # drop yeast.footprints.bed and truncate name to three decimal places
+ tawk 'NR>1{print $1,$2,$3,sprintf("%0.3f",$4)}' yeast.footprints.bed | hgLoadBed -tmpDir=/data/tmp sacCer1 uwFootprintsPrints stdin
+
+ # lift counts to sacSer2 and give back to UW
+ wget http://noble.gs.washington.edu/proj/footprinting/yeast.dnaseI.tagCounts.bed
+ liftOver yeast.dnaseI.tagCounts.bed /hive/data/genomes/sacCer1/bed/blat.sacCer2.2009-02-04/sacCer1ToSacCer2.over.chain.gz /cluster/home/markd/public_html/tmp/yeast/yeast.dnaseI.tagCounts.sacCer2.bed /cluster/home/markd/public_html/tmp/yeast/yeast.dnaseI.tagCounts.sacCer2.nolift.bed
+
+#############################################################################