0f37d4d1e887a759881ddfb77210df9cf6c3acdb
markd
  Sun Jan 16 13:53:12 2022 -0800
inport of All GENCODE VM28

diff --git src/hg/makeDb/doc/mm39/gencode.txt src/hg/makeDb/doc/mm39/gencode.txt
index d64925f..9c34410 100644
--- src/hg/makeDb/doc/mm39/gencode.txt
+++ src/hg/makeDb/doc/mm39/gencode.txt
@@ -102,15 +102,52 @@
     # edit all.joiner to add ~/tmp/gencodeVM28/hgcImportPre.joiner
     # verify with:
     pushd /hive/data/genomes/mm39/bed/gencodeVM28/hgcImportPre
     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
 
 ##############################################################################
+2022-01-16: import of UCSC GENCODE group processing of GENCODE VM28 final (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/gencodeVM28/hgcImport
+    pushd /hive/data/genomes/mm39/bed/gencodeVM28/hgcImport
+
+    (time nice make -kO -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/gencodeGenerateTrackDbs mm39 M28 105 'Oct 2021'
+
+    # 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/gencodeVM28/hgcImport.joiner
+    # verify with:
+    pushd /hive/data/genomes/mm39/bed/gencodeVM28/hgcImport
+    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
+    # add ticket and MARK QA READY
+
+##############################################################################