f86cc1e3f913432f81ad47733aae8e78ab9500c6 markd Mon May 27 12:06:58 2019 -0700 output total number of aligned bases in pslStats -overallStats diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt index c38efd2..813647b 100644 --- src/hg/makeDb/doc/hg19.txt +++ src/hg/makeDb/doc/hg19.txt @@ -33460,16 +33460,46 @@ # itemCount: 38,185 # primaryDataSize: 30,841,362 # primaryIndexSize: 6,892 # zoomLevels: 8 # chromCount: 24 # basesCovered: 580,564,080 # meanDepth (of bases covered): 3.668451 # minDepth: 1.000000 # maxDepth: 81.000000 # std of depth: 5.825349 # link into gbdb mkdir -p /gbdb/hg19/dgv ln -s `pwd`/dgvGold.bb /gbdb/hg19/dgv/ +############################################################################# +2019-05-23: import of UCSC GENCODE group processing of GENCODE V31lift37 (markd) + # import of pre-release, it will be promoted if there are no changes in the final release. + # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions + + # download, build and load tables + mkdir -p /hive/data/genomes/hg19/bed/gencodeV31lift37-pre + pushd /hive/data/genomes/hg19/bed/gencodeV31lift37-pre + (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/gencodeGenerateTrackDbs hg19 31lift37 97 'June 2019' + + # Update human/hg19/wgEncodeGencodeSuper.html and update 'Release Notes' + # to describe new release. [ONLY if it's going to be pushed] + + # edit human/hg19/trackDb.wgEncode.ra to add new .ra file include + make DBS=hg19 + + # edit all.joiner to add ~/tmp/gencodeV31lift37.joiner + # verify with: + pushd /hive/data/genomes/hg19/bed/gencodeV31lift37 + make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck + + # commit all + ##############################################################################