src/hg/makeDb/doc/hg18.txt 1.414

Index: src/hg/makeDb/doc/hg18.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg18.txt,v
retrieving revision 1.413
retrieving revision 1.414
diff -b -B -U 4 -r1.413 -r1.414
--- src/hg/makeDb/doc/hg18.txt	28 Apr 2010 22:35:21 -0000	1.413
+++ src/hg/makeDb/doc/hg18.txt	5 May 2010 00:49:41 -0000	1.414
@@ -16383,8 +16383,38 @@
 
 see file: ucscGenes10.txt
 
 #######################################################################
+# ENCODE Regulation track  (In progress May 2010, very rough instructions
+# as am still defining how to build track...)
+
+      # Create the DNAse peak clusters subtrack.
+      # Get all of the narrowPeak format files for the wgEncodeUwDnaseSeq
+      # unzipped in directory /hive/users/kent/regulate/dnase/peaks
+      cd /hive/users/kent/regulate/dnase
+      ls -1 peaks/*.narrowPeak > peak.lst
+      regClusterMakeTableOfTables peak.lst peak.table
+      regCluster peak.table /dev/null peak.bed
+      awk '$4 > 1 || $5 >= 100' peak.bed > wgEncodeRegDnaseClustered.bed
+      hgLoadBed hg18 wgEncodeRegDnaseClustered wgEncodeRegDnaseClustered.bed
+
+      # Create the Transcription Factor Binding Site subtrack
+      # Get all of the narrowPeak file for wgEncodeYaleChIPseq into tfbs/yale
+      # directory and create all.lst by cutting and pasting 
+      # the file list from
+      # http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeHudsonalphaChipSeq/
+      cd /hive/users/kent/regulate/tfbs/yale
+      grep narrowPeak all. > peak.lst
+      cut -f 2 peak.lst > file.lst
+      foreach i (`cat file.lst`)
+          wget http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeHudsonalphaChipSeq/$i
+      end
+      # Then edit peak.cfg to make sure all cell lines have uniq letters
+      regClusterBedExpCfg peak.lst -encodeList peak.cfg peak.bed peak.exps
+      hgLoadBed hg18 wgEncodeRegTfbsClustered peak.bed
+      hgLoadSqlTab hg18 wgEncodeRegTfbsCells ~/kent/src/hg/lib/expRecord.sql peak.exps
+
+#######################################################################
 # CGAP SAGE (DONE 2007-04-17 Andy)
 
    ssh hgwdev
    bash