55d5984bc5dd9e1d382c811ee9284771925a16b2
kate
  Tue Apr 28 12:37:30 2020 -0700
Assign score field based on tissue medians. refs #25130

diff --git src/hg/makeDb/doc/hg38/gtex.txt src/hg/makeDb/doc/hg38/gtex.txt
index d8e0b72..16d10b5 100644
--- src/hg/makeDb/doc/hg38/gtex.txt
+++ src/hg/makeDb/doc/hg38/gtex.txt
@@ -1,117 +1,145 @@
 #############################################################################
 # GTEx V8 (Apr 2020) Kate
 # Create BED from hgFixed tables (see doc/gtex)
  
 # Load gene models (Gencode V26 transcript union from GTEx)
 
 cd /hive/data/outside/gtex/V8/rnaSeq
 gtfToGenePred gencode.v26.GRCh38.genes.gtf gencodeV26.hg38.genePred \
                 -infoOut=gtexGeneModelInfoV8.tab
 hgLoadGenePred hg38 gtexGeneModelV8 gencodeV26.hg38.genePred
 
 # Get transcript for each gene (why ?)
 tail -n +2 gtexGeneModelInfoV8.tab | awk '{printf("%s\t%s\n", $1, $9)}' > gtexGeneTranscriptsV8.tab
 #hgLoadSqlTab hgFixed gtexTranscriptV8 ~/kent/src/hg/lib/gtexTranscript.sql gtexGeneTranscriptsV8.tab
 # no schema (or table on hgwdev.hgFixed)
 
 # Load BED table
 cd /hive/data/genomes/hg38/bed/gtex
 mkdir V8
 cd V8
 
 set gencode = V26
 ~/kent/src/hg/makeDb/outside/hgGtexGeneBed/hgGtexGeneBed \
-        hg38 -noLoad -gtexVersion=V8 -gencodeVersion=$gencode gtexGeneV8 -verbose=2 >&! log.txt
+        hg38 -noLoad -gtexVersion=V8 -gencodeVersion=$gencode gtexGeneV8 -verbose=2 >&! log.txt &
 
 Reading wgEncodeGencodeAttrs table
 Reading gtexGeneModelV8 table
 Reading gtexTissueMedian table
 Writing tab file gtexGeneV8
 Max score: 267400.000000
 
-~/kent/src/hg/makeDb/outside/hgGtexGeneBed/hgGtexGeneBed \
-        hg38 -gtexVersion=V8 -gencodeVersion=$gencode gtexGeneV8 -verbose=2 
+# Add scores
+set bedScore = ~/kent/src/utils/bedScore/bedScore
+$bedScore -col=10 -minScore=0 -log -method=encode gtexGeneV8.tab gtexGeneBedV8.bed
+textHistogram -real -autoScale=14 -log -col=5 gtexGeneBedV8.bed
+0.000000 ************************************************************ 21287
+71.428643 **************************************************** 5635
+142.857286 **************************************************** 5513
+214.285929 *************************************************** 4683
+285.714571 *************************************************** 4480
+357.143214 *************************************************** 4748
+428.571857 **************************************************** 5466
+500.000500 ************************************************ 3117
+571.429143 ***************************************** 911
+642.857786 ********************************* 252
+714.286429 ************************** 81
+785.715071 ************** 11
+857.143714 ******** 4
+928.572357 *************** 12
+
+# load up
+set lib = ~/kent/src/hg/lib
+hgLoadBed hg38 -noBin -tab -type=bed6+4 \
+        -as=$lib/gtexGeneBed.as -sqlTable=$lib/gtexGeneBed.sql -renameSqlTable \
+                gtexGeneV8 gtexGeneBedV8.bed
+#Read 56200 elements of size 10 from gtexGeneBedV8.bed
+
+
+### TODO 
+# Add GTEx to Gene Sorter (2016-08-18 kate)
+# See hg/near/makeNear.doc
+
 
 #############################################################################
 # GTEx V6 (October 2015) Kate
 # Create BED from hgFixed tables (see doc/gtex)
 # Reloading during QA of track (fixing gene classes, adding scores).  (March 2016) Kate
 
 cd /hive/data/outside/gtex/V6
 
 # see doc/hg19.txt for how this genePred was made
 set chain = /hive/data/genomes/hg19/bed/liftOver/hg19ToHg38.over.chain.gz
 liftOver -genePred gencodeV19.hg19.genePred $chain gtexGeneModelV6.hg38.genePred \
                 gencode.V19.hg38.unmapped
 # 926 unmapped
 hgLoadGenePred hg38 gtexGeneModelV6 gtexGeneModelV6.hg38.genePred
 
 # OLD: creates gtexGeneModelV6.hg38.genePred
 # OLD: NOTE: drops 192 transcripts.  One I spot-checked indeed didn't exist in our hg38 genes
 
 cd /hive/data/genomes/hg38/bed
 mkdir -p gtex
 cd gtex
 
 # table renamed to gtexGeneModel later
 
 # Use latest GENCODE attrs file to get biotypes
 
-
 # create bed table
 ~/kent/src/hg/makeDb/outside/hgGtexGeneBed/hgGtexGeneBed  hg38 -gtexVersion=V6 \
         -noLoad -gencodeVersion=$gencodeVersion gtexGeneBedV6 -verbose=2 >&! makeGeneBed.log
 
 # 45 genes not found in GENCODE attributes table
 
 #Max score: 219385.906250
 
 wc -l *.tab
 wc -l *.tab
 52896 gtexGeneBedV6.tab
 # 55810 gtexGeneBedV6.tab
 
 # exploratory for assigning score based on sum of scores (expScores field)
 set bedScore = ~/kent/src/utils/bedScore/bedScore
 $bedScore -col=10 -minScore=1 -method=std2 gtexGeneBedV6.tab gtexGeneBedV6.std2.bed
 $bedScore -col=10 -minScore=1 -method=encode gtexGeneBedV6.tab gtexGeneBedV6.encode.bed
 $bedScore -col=10 -minScore=1 -method=reg gtexGeneBedV6.tab gtexGeneBedV6.reg.bed
 $bedScore -col=10 -minScore=1 -method=asinh gtexGeneBedV6.tab gtexGeneBedV6.asinh.bed
 
 $bedScore -col=10 -minScore=1 -method=reg -log gtexGeneBedV6.tab gtexGeneBedV6.reg.log.bed
 $bedScore -log -col=10 -minScore=1 -method=std2 gtexGeneBedV6.tab gtexGeneBedV6.std2.log.bed
 $bedScore -log -col=10 -minScore=1 -method=encode gtexGeneBedV6.tab gtexGeneBedV6.encode.log.bed
 $bedScore -log -col=10 -minScore=1 -method=asinh gtexGeneBedV6.tab gtexGeneBedV6.asinh.log.bed
 
 # Using -log -method=encode, as this is closest to density plot of all scores
 # as here: GtexTotalExpressionDensity.png, GtexTotalExpressionFrequency.png
 textHistogram -real -autoScale=14 -log -col=5 gtexGeneBedV6.encode.log.bed
 1.000000 ************************************************************ 22889
 72.357214 *************************************************** 4862
 143.714428 ************************************************** 4199
 215.071643 ************************************************* 3931
 286.428857 ************************************************** 4329
 357.786071 *************************************************** 5419
 429.143285 ************************************************** 4472
 500.500500 ********************************************* 1953
 571.857714 ************************************** 564
 643.214928 ******************************** 200
 714.572142 ************************* 61
 785.929356 *********** 6
 857.286571 ******** 4
 928.643785 ************ 7
 
 $bedScore -col=10 -minScore=0 -log -method=encode gtexGeneBedV6.tab gtexGeneBedV6.bed
 
 
 # load up
 set lib = ~/kent/src/hg/lib
 
 hgLoadBed hg38 -noBin -tab -type=bed6+4 \
         -as=$lib/gtexGeneBed.as -sqlTable=$lib/gtexGeneBed.sql -renameSqlTable \
                 gtexGeneBedNewV6 gtexGeneBedV6.bed
 
 # Add GTEx to Gene Sorter (2016-08-18 kate)
 # See hg/near/makeNear.doc