ec9318204bf7a42acd791c03d0a6f93393843bd7 markd Sun Oct 17 10:12:22 2021 -0700 fixed typo in build doc diff --git src/hg/makeDb/doc/hg19.gencode.txt src/hg/makeDb/doc/hg19.gencode.txt index 81bc1a4..9ca2aeb 100644 --- src/hg/makeDb/doc/hg19.gencode.txt +++ src/hg/makeDb/doc/hg19.gencode.txt @@ -908,31 +908,31 @@ ../../makeDb/outside/gencode/bin/gencodeGenerateTrackDbs hg19 39lift37 105 'Oct 2021' # Update human/hg19/wgEncodeGencodeSuper.html and update 'Release Notes' # to describe new release. # edit human/hg19/trackDb.gencode.ra to add new .ra file include jkmake DBS=hg19 # edit all.joiner to add ~/tmp/gencodeV39lift37.joiner # verify with: pushd /hive/data/genomes/hg19/bed/gencodeV39lift37/hgcImportPre make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck # generates joiner errors The gene/transcript pair is missing from metadata: - ENSG00000168939.6 / ENST00000302805.2 / SPRV3 + ENSG00000168939.6 / ENST00000302805.2 / SPRY3 These are missing from data/release_39lift37/gencode.v39lift37.metadata.Transcript_source.gz data/release_39lift37/gencode.v39lift37.metadata.Gene_source.gz this is the weird cases of SPRV3 which has now has a transcript past the PAR echo -e 'ENST00000302805.2\tensembl_havana_transcript_homo_sapiens' >> tables/wgEncodeGencodeTranscriptSourceV39lift37.tab echo -e 'ENSG00000168939.6\tensembl_havana_transcript_homo_sapiens' >> tables/wgEncodeGencodeGeneSourceV39lift37.tab rm loaded/wgEncodeGencode*Support* (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.4.out& # commit all jkmake alpha DBS=hg19 ##############################################################################