a705056fed4ed3269b4dcbca18194b4f166a36c0
markd
  Fri Oct 15 17:11:33 2021 -0700
import of gencode V39 pre-release

diff --git src/hg/makeDb/doc/hg38/gencode.txt src/hg/makeDb/doc/hg38/gencode.txt
index 844eef5..dff6696 100644
--- src/hg/makeDb/doc/hg38/gencode.txt
+++ src/hg/makeDb/doc/hg38/gencode.txt
@@ -867,15 +867,49 @@
     make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
 
     # check tracks in browser sandbox
     # commit all
     jkmake DBS=hg38 alpha
     # if pushing public: create ticket and MARK QA READY
 
 2021-09-25:
     It was discovered that most of the alt/patch sequence were missing
     this was due switching over to use the ensemblToUcsc table to map
     GENCODE chromosome names for mm39 pre-release.  The code was modified
     to use the assembly report to make the chromosome names and the
     track rebuilt.
     
 #########################################################################
+2021-10-13: import of UCSC GENCODE group processing of GENCODE V39 for hgc all gencode  (markd)
+    # pre-release
+    # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions
+
+    # download, build and load tables
+    mkdir -p /hive/data/genomes/hg38/bed/gencodeV39/hgcImportPre
+    pushd /hive/data/genomes/hg38/bed/gencodeV39/hgcImportPre
+
+    (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out&
+
+    # compare tables from previous release to see if number changed makes
+    # sense.  Results are in gencode-cmp.tsv
+
+    # generate trackDb and joiner blurb
+    pushd ~/kent/src/hg/makeDb/trackDb
+    ../outside/gencode/bin/gencodeGenerateTrackDbs  hg38 39 105 'Sept 2021'
+
+    # Update 'Release Notes' (for final)
+    # human/hg38/wgEncodeGencodeSuper.html
+
+    # edit human/hg38/trackDb.gencode.ra to add new .ra file include
+    jkmake DBS=hg38
+
+    # edit all.joiner to add ~/tmp/gencodeV39.joiner
+    # verify with:
+    pushd /hive/data/genomes/hg38/bed/gencodeV39/hgcImportPre
+    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
+
+    # check tracks in browser sandbox
+    # commit all
+    jkmake DBS=hg38 alpha
+    # if pushing public: create ticket and MARK QA READY
+
+#########################################################################