b59391a116347bd32c8d20f829abe3e75cf5cf51
kate
  Mon Aug 29 16:17:32 2016 -0700
Finish hg38 GTEx in gene sorter. refs #17288

diff --git src/hg/near/makeNear.doc src/hg/near/makeNear.doc
index a5607ae..7fdef6d 100644
--- src/hg/near/makeNear.doc
+++ src/hg/near/makeNear.doc
@@ -630,45 +630,44 @@
    affyExonTissuesGs.ra affyExonTissuesGsMedian mm8.affyExonTissuesGsMedianExps
 hgExpDistance mm8 affyExonTissuesGsMedian \
    affyExonTissuesGsMedianExps affyExonTissuesGsMedianDist
 
 ###############################################################
 ## GTEx
 ## (2016-08-16, kate)
 
 # Create a table that maps between known genes and GTEx (GENCODE V19) gene ids
 cd /hive/data/genomes/hg19/bed/gtex
 
 #hgMapToGene hg19 -type=genePred gtexGeneModelV6 knownGene knownToGtex
 hgMapToGene hg19 -noLoad -all -type=genePred gtexGeneModelV6 knownGene knownToGtex.all
 hgMapToGene hg19 -all -type=genePred gtexGeneModelV6 knownGene knownToGtex
 
-#hgMapToGene hg38 -type=genePred gtexGeneModelV6 knownGene knownToGtex
-hgMapToGene hg38 -all -type=genePred gtexGeneModelV6 knownGene knownToGtex
-
 # Create expression distance table from median table.  This will take about an hour.
 #cd ~/src/hg/near/hgExpDistance
-# TODO: Consider adding weights file
-
+# edit to downweight brain to .5 (13 tissues total)
 hgsql hgFixed -e select 1.0, id, name from gtexTissue > gtex.weights
-# edit to downweight brain (13 tissues total)
-
-hgExpDistance hg19 -verbose=2 -lookup=knownToGtex -weights=gtex.weights \
-        hgFixed.gtexTissueMedian hgFixed.gtexTissue \
-                gtexDistance
-
 hgExpDistance hg19 -verbose=2 -lookup=knownToGtex -weights=gtex.weights \
         hgFixed.gtexTissueMedian hgFixed.gtexTissue \
                 gtexDistance
 
 # Create ratio table.  
 # TODO: Consider adding -clump file
 # Defaults for microarray are too high -- RPKM is significant >2 roughly
 hgRatioMicroarray -minAbsVal=2 -minMaxVal=5 -database=hgFixed gtexTissueMedian gtexTissueMedianRatio2
 
 # Get max scores for columnDb.ra
 hgMaxExp hgFixed gtexTissueMedian
 # 219385.91
  
 hgMaxExp hgFixed gtexTissueMedianRatio
 # 12.53
 
+cd /hive/data/genomes/hg38/bed/gtex
+#hgMapToGene hg38 -type=genePred gtexGeneModelV6 knownGene knownToGtex
+hgMapToGene hg38 -all -type=genePred gtexGeneModelV6 knownGene knownToGtex
+
+hgExpDistance hg38 -verbose=2 -lookup=knownToGtex -weights=gtex.weights \
+        hgFixed.gtexTissueMedian hgFixed.gtexTissue \
+                gtexDistance
+# 4 hours ?
+