9a2b57b9b8f4d0db31b00a238a0047c6f25323bf
kate
  Thu Apr 23 10:33:51 2020 -0700
Fixing some typos

diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt
index 053d9bf..80ec8c1 100644
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@ -30783,35 +30783,35 @@
 
 #############################################################################
 # GTEx V6 (October 2015) Kate
 # Create BED from hgFixed tables (see doc/gtex)
 # Reload with scores (see hg38/gtex.txt)
 
 cd /hive/data/outside/gtex/V6
 
 # Load gene models (Gencode V19 transcript union from GTEx)
 gunzip gencode.v19.genes.patched_contigs.gtf.gz
 
 # NOTE FOR NEXT TIME: hg19 now has chrMT, so leave "chrMT" as-is instead of changing to chrM.
 # optional: liftOver from chrMT (NC_012920) coords to chrM (NC_001807).
 
 awk '$1 !~ /^#/ {print "chr"$0}' gencode.v19.genes.patched_contigs.gtf | sed 's/chrMT/chrM/' | \
-        gtfToGenePred stdin gencodeV19.hg19.genePred
-hgLoadGenePred hg19 gtexGeneModelV6 gencodeV19.hg19.genePred -infoOut=gtexGeneModelInfoV6.tab
+        gtfToGenePred stdin gencodeV19.hg19.genePred -infoOut=gtexGeneModelInfoV6.tab
+hgLoadGenePred hg19 gtexGeneModelV6 gencodeV19.hg19.genePred
 
 # Get transcript for each gene
-A#tail -n +2 gtexGeneModelInfoV6.tab | awk '{printf("%s\t%s\n", $1, $9)}' > gtexGeneTranscriptsV6.tab
+#tail -n +2 gtexGeneModelInfoV6.tab | awk '{printf("%s\t%s\n", $1, $9)}' > gtexGeneTranscriptsV6.tab
 #hgLoadSqlTab hgFixed gtexTranscriptV6 ~/kent/src/hg/lib/gtexTranscript.sql gtexGeneTranscriptsV6.tab
 
 # Load BED table
 cd /hive/data/genomes/hg19/bed
 mkdir -p gtex
 cd gtex
 
 set gencode = V24lift37
 # use latest attribute annotaion
 ~/kent/src/hg/makeDb/outside/hgGtexGeneBed/hgGtexGeneBed \
         hg19 -noLoad -gtexVersion=V6 -gencodeVersion=$gencode gtexGeneV6 >&! log.txt
 #Max score: 219385.906250
 # 925 genes not found in GencodeAttrs table
 wc -l gtexGeneV6.tab
 # 55393 gtexGeneV6.tab