d87e5f63bc000d560c21bca638b6d5f3dee0173d
kate
  Wed Apr 3 12:06:45 2019 -0700
Add scripts and make docs for ENCODE 3 TF binding site tracks. refs #21139

diff --git src/hg/makeDb/doc/encodeRegHg19.txt src/hg/makeDb/doc/encodeRegHg19.txt
index 1196a19..d1a59a2 100644
--- src/hg/makeDb/doc/encodeRegHg19.txt
+++ src/hg/makeDb/doc/encodeRegHg19.txt
@@ -1070,30 +1070,31 @@
     bedSort clusters.target.bed clusters.target.sorted.bed
     /cluster/bin/x86_64/bedToBigBed -type=bed15 -tab clusters.target.sorted.bed \
         /hive/data/genomes/hg19/chrom.sizes $track.bb
     # Error line 1 of xx.bed: expecting 690 elements in expIds list (bed field 14)
     # Might be a bogus error -- looks OK on inspection
     # GOT HERE
     ln -s `pwd`/$track.bb /gbdb/hg19/wgEncodeReg
     hgBbiDbLink hg19 $track wg/gbdb/hg19/wgEncodeReg/$track.bb
 
 # for now, adding maxWindowToDraw 1M setting to trackDb to limit performance hit
 
 # shrink table format to BED5+, with columns 6 and 7 non-sparse comma-sep lists
 # of exp id's and scores
 
     clusterShrinkExps.pl clusters.target.sorted.bed > clusters.shrunk.bed
+# NOTE: moving this tool to makeDb/hgBedsToBedExps/bedExpsToFactorSource.pl
 
     hgLoadBed -sqlTable=~/kent/src/hg/lib/factorSource.sql -renameSqlTable \
         hg19 wgEncodeRegTfbsClusteredShrunkMini test.shrink.bed
 
     hgLoadBed -sqlTable=~/kent/src/hg/lib/factorSource.sql -renameSqlTable \
         hg19 wgEncodeRegTfbsClusteredShrunk clusters.shrunk.bed
 
 # rename Shrunk to V3
 # copy to downloads
     cp clusters.shrunk.bed downloads/wgEncodeRegTfbsClusteredV3.bed
     cd downloads
     gzip wgEncodeRegTfbsClusteredV3.bed
 
     cd /hive/groups/encode/dcc/pipeline/downloads/hg19/wgEncodeRegTfbsClustered/releaseLatest
     md5sum wgEncodeRegTfbsClusteredV3.bed >> md5sum.txt