2e85d518a6bc169b901b3c0b57e24b45694296fc
markd
  Tue Jun 29 16:05:38 2021 -0700
update GENCODE VM27 from pre-release from final

diff --git src/hg/makeDb/doc/mm39/gencode.txt src/hg/makeDb/doc/mm39/gencode.txt
index 4c397da..202cdd3 100644
--- src/hg/makeDb/doc/mm39/gencode.txt
+++ src/hg/makeDb/doc/mm39/gencode.txt
@@ -1,78 +1,79 @@
 ##############################################################################
 2021-03-12: import of UCSC GENCODE group processing of GENCODE VM26 (markd)
     # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions
     # download, build and load tables
     mkdir -p /hive/data/genomes/mm39/bed/gencodeVM26
     pushd /hive/data/genomes/mm39/bed/gencodeVM26
 
     (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
     ../../makeDb/outside/gencode/bin/gencodeGenerateTrackDbsOldSchema mm39 M26 103 'Feb 2021'
 
     # If being pushed public, update 'Release Notes' in
     # mouse/mm39/wgEncodeGencodeSuper.html
 
     # edit human/mm39/trackDb.gencode.ra to add new .ra file include
     jkmake DBS=mm39
 
     ## only if being pushed to RR:
     # edit all.joiner to add ~/tmp/gencodeVM26.joiner
     # verify with:
     pushd /hive/data/genomes/mm39/bed/gencodeVM26
     make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
 
        Error: 55597 of 140725 elements (39.508%) of mm39.wgEncodeGencodeAttrsVM26.transcriptId are not in key wgEncodeGencodeExonSupportVM26.transcriptId line 5880 of /cluster/home/markd/kent/src/hg/makeDb/schema/all.joiner
        Error: 55597 of 140725 elements (39.508%) of mm39.wgEncodeGencodeAttrsVM26.transcriptId are not in key wgEncodeGencodeExonSupportVM26.transcriptId line 5880 of /cluster/home/markd/kent/src/hg/makeDb/schema/all.joiner
 
     # however, these are not currently used by the browser, so modify joiner check. Check
     # with GENCODE is this is expected, might be a cleanup on move to mm39
 
 
     # check tracks in browser sandbox
     # commit all
     make DBS=mm39 alpha
     # if pushing public: add ticket and MARK QA READY
 
 ##############################################################################
-2021-04-06: import of UCSC GENCODE group processing of GENCODE VM27 (markd)
+2021-06-29: import of UCSC GENCODE group processing of GENCODE VM27 (markd)
+    update from 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/mm39/bed/gencodeVM27Pre
-    pushd /hive/data/genomes/mm39/bed/gencodeVM27Pre
+    mkdir -p /hive/data/genomes/mm39/bed/gencodeVM27
+    pushd /hive/data/genomes/mm39/bed/gencodeVM27
 
     (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
-    ../../makeDb/outside/gencode/bin/gencodeGenerateTrackDbsOldSchema mm39 M27 104 'Apr 2021'
+    ../../makeDb/outside/gencode/bin/gencodeGenerateTrackDbsOldSchema mm39 M27 104 'May 2021'
 
-    # If being pushed public, update 'Release Notes' in
+    # Update 'Release Notes' in
     # mouse/mm39/wgEncodeGencodeSuper.html
 
     # edit human/mm39/trackDb.gencode.ra to add new .ra file include
     jkmake DBS=mm39
 
     ## only if being pushed to RR:
     # edit all.joiner to add ~/tmp/gencodeVM27.joiner
     # verify with:
-    pushd /hive/data/genomes/mm39/bed/gencodeVM27Pre
+    pushd /hive/data/genomes/mm39/bed/gencodeVM27
     make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
 
     # however, these are not currently used by the browser, so modify joiner check. Check
     # with GENCODE is this is expected, might be a cleanup on move to mm39
 
 
     # check tracks in browser sandbox
     # commit all
     make DBS=mm39 alpha
     # if pushing public: add ticket and MARK QA READY
 
 ##############################################################################