aa4117a4a17ef2851a89e2132bba5d11bd4bf5b5
kate
  Wed Feb 3 10:56:39 2021 -0800
Add make doc for targetScan V7.2. refs #26287

diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt
index 4b9bc09..fd37668 100644
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@ -14167,30 +14167,63 @@
     ssh hgwdev
     mkdir -p /cluster/data/hg19/bed/targetScanS
     cd /cluster/data/hg19/bed/targetScanS
 
     wget --timestamping http://www.targetscan.org/vert_50/ucsc/hg19/hg19Cons_ALL_CHRS.BED
 
     hgLoadBed hg19 targetScanS hg19Cons_ALL_CHRS.BED
     #	Loaded 54199 elements of size 6
     featureBits hg19 targetScanS
     #   354163 bases of 2897316137 (0.012%) in intersection
 
     # Create/edit/check in targetScans.html and trackDb.ra under
     # kent/src/hg/makeDb/trackDb/human/hg19
 
 ##########################################################################
+# Update targetScanS track to Version 7.2 - (DONE 2021-02-03 Brittney & Kate)
+
+cd /hive/data/genomes/hg19/bed/targetScanS
+mkdir vert_72
+
+wget --header="accept-encoding: gzip" http://www.targetscan.org/vert_72/vert_72_data_download/Predicted_Target_Locations.default_predictions.hg19.bed.zip 
+
+unzip Predicted_Target_Locations.default_predictions.hg19.bed.zip 
+
+# The downloaded file is a BED12. The score column has values between -1 and 100. 
+# Everything else looks good.
+# Create a new BED12+1 file with this score value as field 13 and change the score values 
+# to 0 in column 5.
+
+awk 'OFS="\t" {c=$5; $5="0"; print $0, c}' \
+        < Predicted_Target_Locations.default_predictions.hg19.bed
+        > bed12+1_targetScanSitesV72.bed
+
+# copy "bedDetail.as" from ~/kent/src/hg/lib and rename to targetScanS.as and edit to 
+# match our new BED12+1 file. 
+cp ~/kent/src/hg/lib/bedDetail.as .
+mv bedDetail.as targetScanS.as    
+
+bedToBigBed -type=bed12+1 -as=targetScanS.as bed12+1_targetScanSitesV72.bed \
+        ../../../chrom.sizes targetScanSitesV72.bb
+
+# Link bigBed file into /gbdb directory for access by browser
+cd /gbdb/hg19
+mkdir targetScan
+cd targetScan
+ln -s /hive/data/genomes/hg19/bed/targetScanS/vert_72/targetScanSitesV72.bb .
+
+##########################################################################
 # Neandertal tracks for hg19 (DONE - 2010-12-14 - Hiram)
     # data supplied by Ed Green into /hive/data/outside/homNea/hg19
     # add Neandertal group to hg19 grp
     hgsql hg19 -e \
       "insert into grp values ('neandertal', 'Neandertal Assembly and Analysis', 6.5, 1);"
 
     mkdir -p /hive/data/genomes/hg19/bed/homNea/seqAlis
     cd /hive/data/genomes/hg19/bed/homNea/seqAlis
 
 for T in Feld1 Mez1 Sid1253 Vi33.16 Vi33.25 Vi33.26
 do
     ln -s /hive/data/outside/homNea/hg19/${T}.hg18.bam \
 	./SL${T}.hg19.bam
 done