8fb72c8da4d09c44c56388251370428af1868adf
lrnassar
  Thu Dec 19 15:59:42 2024 -0800
Adding the ENCODE 4 TF track, refs #34930

diff --git src/hg/makeDb/doc/hg38/hg38.txt src/hg/makeDb/doc/hg38/hg38.txt
index 785751c..1f3dc12 100644
--- src/hg/makeDb/doc/hg38/hg38.txt
+++ src/hg/makeDb/doc/hg38/hg38.txt
@@ -7366,15 +7366,25 @@
 
     sed -e 's/^/    # /;' fb.GCF_009762305.2.chainRBest.Hg38.txt
     # 1461710350 bases of 2409685272 (60.660%) in intersection
 
 ##############################################################################
 # hg38.chromAlias.bb was incorrectly built without indexes so it will not
 # work with bedToBigBed 2024-04-08 markd
 
 cd /hive/data/genomes/hg38/goldenPath/bigZips/initial
 mv hg38.chromAlias.bb  hg38.chromAlias.noindexes.bb
 bigBedInfo -asOut hg38.chromAlias.noindexes.bb >hg38.chromAlias.as
 bigBedToBed hg38.chromAlias.noindexes.bb  hg38.chromAlias.bed
 bedToBigBed -tab -type=bed3+ -as=hg38.chromAlias.as hg38.chromAlias.bed -sizesIs2Bit  -extraIndex=ucsc,assembly,ensembl,genbank,refseq hg38.2bit hg38.chromAlias.bb
 
 ##############################################################################
+
+# ENCODE 4 TF rPeak Clusters - RM #34930 - Lou 12/19/24
+
+mkdir /hive/data/genomes/hg38/bed/ENCODEv4TFrPeaks
+cd /hive/data/genomes/hg38/bed/ENCODEv4TFrPeaks
+hubClone -download https://users.wenglab.org/gaomingshi/TF.rpeak.test.txt
+ln -s /hive/data/genomes/hg38/bed/ENCODEv4TFrPeaks/no_trim.TF_name.rPeaks.bb /gbdb/hg38/bbi/ENCODE4/TFrPeakClusters.bb
+ln -s /hive/data/genomes/hg38/bed/ENCODEv4TFrPeaks/no_trim.TF_name.decorator.bb /gbdb/hg38/bbi/ENCODE4/TFrPeakClustersDecorator.bb
+# Then just moved the files to the ENCODEv4TFrPeaks dir, moved/tweaked HTML and trackDb
+