dfa6639914399df4d023ebc3df4f4009238c645e
kate
  Mon May 4 16:50:39 2020 -0700
Fix chron order in make doc. refs #25130

diff --git src/hg/makeDb/doc/hg38/gtex.txt src/hg/makeDb/doc/hg38/gtex.txt
index 16d10b5..5a5303e 100644
--- src/hg/makeDb/doc/hg38/gtex.txt
+++ src/hg/makeDb/doc/hg38/gtex.txt
@@ -1,79 +1,16 @@
 #############################################################################
-# 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 &
-
-Reading wgEncodeGencodeAttrs table
-Reading gtexGeneModelV8 table
-Reading gtexTissueMedian table
-Writing tab file gtexGeneV8
-Max score: 267400.000000
-
-# 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
@@ -130,16 +67,76 @@
 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
 
+#############################################################################
+# 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 &
+
+Reading wgEncodeGencodeAttrs table
+Reading gtexGeneModelV8 table
+Reading gtexTissueMedian table
+Writing tab file gtexGeneV8
+Max score: 267400.000000
 
+# 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