0df7d8fdb7c40a393e33791956a8c98ab460dead markd Thu May 23 10:54:50 2019 -0700 import mouse GENCODE VM22 pre-release diff --git src/hg/makeDb/schema/all.joiner src/hg/makeDb/schema/all.joiner index 0e29e9d..263c41f 100644 --- src/hg/makeDb/schema/all.joiner +++ src/hg/makeDb/schema/all.joiner @@ -962,31 +962,31 @@ identifier wgEncodeGencodeUniProtV10 "Link together Gencode UniProt Support table with Attributes table" hg19.wgEncodeGencodeUniProtV10.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV10.transcriptId minCheck=0.358209 identifier wgEncodeGencodeAnnotationRemarkV10 "Link together Gencode Annotation Remark table with Attributes table" hg19.wgEncodeGencodeAnnotationRemarkV10.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV10.transcriptId minCheck=0.10 # end Gencode V10 # begin Gencode V11 # gencode genepreds with no associations -# wgEncodeGencodePolyaV11 +# wgencodegencodepolyav11 # wgEncodeGencode2wayConsPseudoV11 # gencode genepreds with joining through wgEncodeGencodeAttrsV11 identifier wgEncodeGencodeBasicAttrsV11 "Link together Gencode Basic Table with Attributes table" hg19.wgEncodeGencodeAttrsV11.transcriptId hg19.wgEncodeGencodeBasicV11.name identifier wgEncodeGencodeCompAttrsV11 "Link together Gencode Comprehensive Table with Attributes table" hg19.wgEncodeGencodeAttrsV11.transcriptId hg19.wgEncodeGencodeCompV11.name identifier wgEncodeGencodePseudoGeneAttrsV11 "Link together Gencode PseudoGene Table with Attributes table" @@ -2428,30 +2428,126 @@ hg38.wgEncodeGencodeAnnotationRemarkV30.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV30.transcriptId minCheck=0.10 identifier wgEncodeGencodeEntrezGeneV30 "Link together Gencode UniProt Support table with Attributes table" hg38.wgEncodeGencodeEntrezGeneV30.transcriptId dupeOk hg38.wgEncodeGencodeEntrezGeneV30.transcriptId minCheck=0.358209 identifier wgEncodeGencodeExonSupportV30 "Link together Gencode Exon Support table with Attributes table" hg38.wgEncodeGencodeExonSupportV30.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV30.transcriptId minCheck=0.95 # end Gencode V30 +# begin Gencode V31 + +# gencode genePred tables with no associations +# wgEncodeGencodePolyaV31 +# wgEncodeGencode2wayConsPseudoV31 + +# gencode genePred tables with joining through wgEncodeGencodeAttrsV31 +identifier wgEncodeGencodeBasicAttrsV31 +"Link together Gencode Basic Table with Attributes table" + hg38.wgEncodeGencodeAttrsV31.transcriptId + hg38.wgEncodeGencodeBasicV31.name + +identifier wgEncodeGencodeCompAttrsV31 +"Link together Gencode Comprehensive Table with Attributes table" + hg38.wgEncodeGencodeAttrsV31.transcriptId + hg38.wgEncodeGencodeCompV31.name + +identifier wgEncodeGencodePseudoGeneAttrsV31 +"Link together Gencode PseudoGene Table with Attributes table" + hg38.wgEncodeGencodeAttrsV31.transcriptId + hg38.wgEncodeGencodePseudoGeneV31.name + +# gencode association tables (joined through wgEncodeGencodeAttrsV31) +identifier wgEncodeGencodeGeneSourceV31 +"Link together Gencode Gene Source table with Attributes table" + hg38.wgEncodeGencodeGeneSourceV31.geneId + hg38.wgEncodeGencodeAttrsV31.geneId + +identifier wgEncodeGencodeGeneSymbolV31 +"Link together Gencode gene symbol table with Attributes table" + hg38.wgEncodeGencodeGeneSymbolV31.transcriptId dupeOk + hg38.wgEncodeGencodeAttrsV31.transcriptId minCheck=0.20 + +identifier wgEncodeGencodePdbV31 +"Link together Gencode Pdb table with Attributes table" + hg38.wgEncodeGencodePdbV31.transcriptId dupeOk + hg38.wgEncodeGencodeAttrsV31.transcriptId minCheck=0.015 + +identifier wgEncodeGencodePubMedV31 +"Link together Gencode Pubmed table with Attributes table" + hg38.wgEncodeGencodePubMedV31.transcriptId dupeOk + hg38.wgEncodeGencodeAttrsV31.transcriptId minCheck=0.63 + +identifier wgEncodeGencodeRefSeqV31 +"Link together Gencode RefSeq table with Attributes table" + hg38.wgEncodeGencodeRefSeqV31.transcriptId dupeOk + hg38.wgEncodeGencodeAttrsV31.transcriptId minCheck=0.05 + +identifier wgEncodeGencodeRefSeqToRefGeneV31 +"Link together Gencode RefSeq table with refGene track" + hg38.wgEncodeGencodeRefSeqV31.rnaAcc dupeOk chopAfter=. + hg38.refGene.name minCheck=0.77 + +identifier wgEncodeGencodeTagV31 +"Link together Gencode Tag table with Attributes table" + hg38.wgEncodeGencodeTagV31.transcriptId dupeOk + hg38.wgEncodeGencodeAttrsV31.transcriptId minCheck=0.373378 + hg38.wgEncodeGencodeRefSeqV31.transcriptId minCheck=0.9 + +identifier wgEncodeGencodeTranscriptSourceV31 +"Link together Gencode Transcript Source table with Attributes table" + hg38.wgEncodeGencodeTranscriptSourceV31.transcriptId + hg38.wgEncodeGencodeAttrsV31.transcriptId + +identifier wgEncodeGencodeTranscriptSupportV31 +"Link together Gencode Transcript Support table with Attributes table" + hg38.wgEncodeGencodeTranscriptSupportV31.transcriptId dupeOk + hg38.wgEncodeGencodeAttrsV31.transcriptId minCheck=0.20 + +identifier wgEncodeGencodeTranscriptionSupportLevelV31 +"Link together Gencode Transcription Support Level table with Attributes table" + hg38.wgEncodeGencodeTranscriptionSupportLevelV31.transcriptId dupeOk + hg38.wgEncodeGencodeAttrsV31.transcriptId minCheck=0.30 + +identifier wgEncodeGencodeUniProtV31 +"Link together Gencode UniProt Support table with Attributes table" + hg38.wgEncodeGencodeUniProtV31.transcriptId dupeOk + hg38.wgEncodeGencodeAttrsV31.transcriptId minCheck=0.358209 + +identifier wgEncodeGencodeAnnotationRemarkV31 +"Link together Gencode Annotation Remark table with Attributes table" + hg38.wgEncodeGencodeAnnotationRemarkV31.transcriptId dupeOk + hg38.wgEncodeGencodeAttrsV31.transcriptId minCheck=0.10 + +identifier wgEncodeGencodeEntrezGeneV31 +"Link together Gencode UniProt Support table with Attributes table" + hg38.wgEncodeGencodeEntrezGeneV31.transcriptId dupeOk + hg38.wgEncodeGencodeEntrezGeneV31.transcriptId minCheck=0.358209 + +identifier wgEncodeGencodeExonSupportV31 +"Link together Gencode Exon Support table with Attributes table" + hg38.wgEncodeGencodeExonSupportV31.transcriptId dupeOk + hg38.wgEncodeGencodeAttrsV31.transcriptId minCheck=0.90 + +# end Gencode V31 + # begin Gencode V24lift37 # gencode genepreds with no associations # wgEncodeGencodePolyaV24lift37 # wgEncodeGencode2wayConsPseudoV24lift37 # gencode genepreds with joining through wgEncodeGencodeAttrsV24lift37 identifier wgEncodeGencodeBasicAttrsV24lift37 "Link together Gencode Basic Table with Attributes table" hg19.wgEncodeGencodeAttrsV24lift37.transcriptId hg19.wgEncodeGencodeBasicV24lift37.name identifier wgEncodeGencodeCompAttrsV24lift37 "Link together Gencode Comprehensive Table with Attributes table" hg19.wgEncodeGencodeAttrsV24lift37.transcriptId @@ -4091,30 +4187,126 @@ mm10.wgEncodeGencodeAnnotationRemarkVM21.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM21.transcriptId minCheck=0.10 identifier wgEncodeGencodeEntrezGeneVM21 "Link together Gencode UniProt Support table with Attributes table" mm10.wgEncodeGencodeEntrezGeneVM21.transcriptId dupeOk mm10.wgEncodeGencodeEntrezGeneVM21.transcriptId minCheck=0.358209 identifier wgEncodeGencodeExonSupportVM21 "Link together Gencode Exon Support table with Attributes table" mm10.wgEncodeGencodeExonSupportVM21.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM21.transcriptId minCheck=0.95 # end Gencode VM21 +# begin Gencode VM22 + +# gencode genePred tables with no associations +# wgEncodeGencodePolyaVM22 +# wgEncodeGencode2wayConsPseudoVM22 + +# gencode genePred tables with joining through wgEncodeGencodeAttrsVM22 +identifier wgEncodeGencodeBasicAttrsVM22 +"Link together Gencode Basic Table with Attributes table" + mm10.wgEncodeGencodeAttrsVM22.transcriptId + mm10.wgEncodeGencodeBasicVM22.name + +identifier wgEncodeGencodeCompAttrsVM22 +"Link together Gencode Comprehensive Table with Attributes table" + mm10.wgEncodeGencodeAttrsVM22.transcriptId + mm10.wgEncodeGencodeCompVM22.name + +identifier wgEncodeGencodePseudoGeneAttrsVM22 +"Link together Gencode PseudoGene Table with Attributes table" + mm10.wgEncodeGencodeAttrsVM22.transcriptId + mm10.wgEncodeGencodePseudoGeneVM22.name + +# gencode association tables (joined through wgEncodeGencodeAttrsVM22) +identifier wgEncodeGencodeGeneSourceVM22 +"Link together Gencode Gene Source table with Attributes table" + mm10.wgEncodeGencodeGeneSourceVM22.geneId + mm10.wgEncodeGencodeAttrsVM22.geneId + +identifier wgEncodeGencodeGeneSymbolVM22 +"Link together Gencode gene symbol table with Attributes table" + mm10.wgEncodeGencodeGeneSymbolVM22.transcriptId dupeOk + mm10.wgEncodeGencodeAttrsVM22.transcriptId minCheck=0.20 + +identifier wgEncodeGencodePdbVM22 +"Link together Gencode Pdb table with Attributes table" + mm10.wgEncodeGencodePdbVM22.transcriptId dupeOk + mm10.wgEncodeGencodeAttrsVM22.transcriptId minCheck=0.015 + +identifier wgEncodeGencodePubMedVM22 +"Link together Gencode Pubmed table with Attributes table" + mm10.wgEncodeGencodePubMedVM22.transcriptId dupeOk + mm10.wgEncodeGencodeAttrsVM22.transcriptId minCheck=0.63 + +identifier wgEncodeGencodeRefSeqVM22 +"Link together Gencode RefSeq table with Attributes table" + mm10.wgEncodeGencodeRefSeqVM22.transcriptId dupeOk + mm10.wgEncodeGencodeAttrsVM22.transcriptId minCheck=0.05 + +identifier wgEncodeGencodeRefSeqToRefGeneVM22 +"Link together Gencode RefSeq table with refGene track" + mm10.wgEncodeGencodeRefSeqVM22.rnaAcc dupeOk chopAfter=. + mm10.refGene.name minCheck=0.77 + +identifier wgEncodeGencodeTagVM22 +"Link together Gencode Tag table with Attributes table" + mm10.wgEncodeGencodeTagVM22.transcriptId dupeOk + mm10.wgEncodeGencodeAttrsVM22.transcriptId minCheck=0.36 + mm10.wgEncodeGencodeRefSeqVM22.transcriptId minCheck=0.9 + +identifier wgEncodeGencodeTranscriptSourceVM22 +"Link together Gencode Transcript Source table with Attributes table" + mm10.wgEncodeGencodeTranscriptSourceVM22.transcriptId + mm10.wgEncodeGencodeAttrsVM22.transcriptId + +identifier wgEncodeGencodeTranscriptSupportVM22 +"Link together Gencode Transcript Support table with Attributes table" + mm10.wgEncodeGencodeTranscriptSupportVM22.transcriptId dupeOk + mm10.wgEncodeGencodeAttrsVM22.transcriptId minCheck=0.20 + +identifier wgEncodeGencodeTranscriptionSupportLevelVM22 +"Link together Gencode Transcription Support Level table with Attributes table" + mm10.wgEncodeGencodeTranscriptionSupportLevelVM22.transcriptId dupeOk + mm10.wgEncodeGencodeAttrsVM22.transcriptId minCheck=0.30 + +identifier wgEncodeGencodeUniProtVM22 +"Link together Gencode UniProt Support table with Attributes table" + mm10.wgEncodeGencodeUniProtVM22.transcriptId dupeOk + mm10.wgEncodeGencodeAttrsVM22.transcriptId minCheck=0.35 + +identifier wgEncodeGencodeAnnotationRemarkVM22 +"Link together Gencode Annotation Remark table with Attributes table" + mm10.wgEncodeGencodeAnnotationRemarkVM22.transcriptId dupeOk + mm10.wgEncodeGencodeAttrsVM22.transcriptId minCheck=0.10 + +identifier wgEncodeGencodeEntrezGeneVM22 +"Link together Gencode UniProt Support table with Attributes table" + mm10.wgEncodeGencodeEntrezGeneVM22.transcriptId dupeOk + mm10.wgEncodeGencodeEntrezGeneVM22.transcriptId minCheck=0.35 + +identifier wgEncodeGencodeExonSupportVM22 +"Link together Gencode Exon Support table with Attributes table" + mm10.wgEncodeGencodeExonSupportVM22.transcriptId dupeOk + mm10.wgEncodeGencodeAttrsVM22.transcriptId minCheck=0.90 + +# end Gencode VM22 + identifier wgEncodeGencodeClassesV3Hg19 "Link together Gencode gene model (Known) and class for July 2009 Data Version" hg19.wgEncodeGencodeClassesV3.name hg19.wgEncodeGencodeAutoV3.name unique hg19.wgEncodeGencodeManualV3.name unique hg19.wgEncodeGencodePolyaV3.name unique identifier acemblyName dependency "Link together Acembly gene model structure and peptide." $hg,$mm.acembly.name $hg,!hg17,$mm.acemblyPep.name unique minCheck=0.90 hg17.acemblyPep.name unique minCheck=0.63 $hg,$mm.acemblyClass.name full unique identifier ECgeneName dependency