703e07e1d02ee1e346d5dcf6c0610a3d4d5f4069 markd Tue Jun 29 17:12:38 2021 -0700 import of GENCODE V38lift37 diff --git src/hg/makeDb/schema/all.joiner src/hg/makeDb/schema/all.joiner index 5223906..eaba16f 100644 --- src/hg/makeDb/schema/all.joiner +++ src/hg/makeDb/schema/all.joiner @@ -3088,30 +3088,125 @@ hg38.wgEncodeGencodeAnnotationRemarkV37.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV37.transcriptId minCheck=0.10 identifier wgEncodeGencodeEntrezGeneV37 "Link together Gencode UniProt Support table with Attributes table" hg38.wgEncodeGencodeEntrezGeneV37.transcriptId dupeOk hg38.wgEncodeGencodeEntrezGeneV37.transcriptId minCheck=0.35 identifier wgEncodeGencodeExonSupportV37 "Link together Gencode Exon Support table with Attributes table" hg38.wgEncodeGencodeExonSupportV37.transcriptId dupeOk hg38.wgEncodeGencodeAttrsV37.transcriptId minCheck=0.80 # end Gencode V37 +# begin Gencode V38 + +# gencode genePred tables with no associations +# wgEncodeGencodePolyaV38 +# wgEncodeGencode2wayConsPseudoV38 + +# gencode genePred tables with joining through wgEncodeGencodeAttrsV38 +identifier wgEncodeGencodeBasicAttrsV38 +"Link together Gencode Basic Table with Attributes table" + hg38.wgEncodeGencodeAttrsV38.transcriptId + hg38.wgEncodeGencodeBasicV38.name + +identifier wgEncodeGencodeCompAttrsV38 +"Link together Gencode Comprehensive Table with Attributes table" + hg38.wgEncodeGencodeAttrsV38.transcriptId + hg38.wgEncodeGencodeCompV38.name + +identifier wgEncodeGencodePseudoGeneAttrsV38 +"Link together Gencode PseudoGene Table with Attributes table" + hg38.wgEncodeGencodeAttrsV38.transcriptId + hg38.wgEncodeGencodePseudoGeneV38.name + +# gencode association tables (joined through wgEncodeGencodeAttrsV38) +identifier wgEncodeGencodeGeneSourceV38 +"Link together Gencode Gene Source table with Attributes table" + hg38.wgEncodeGencodeGeneSourceV38.geneId + hg38.wgEncodeGencodeAttrsV38.geneId + +identifier wgEncodeGencodeGeneSymbolV38 +"Link together Gencode gene symbol table with Attributes table" + hg38.wgEncodeGencodeGeneSymbolV38.transcriptId dupeOk + hg38.wgEncodeGencodeAttrsV38.transcriptId minCheck=0.20 + +identifier wgEncodeGencodePdbV38 +"Link together Gencode Pdb table with Attributes table" + hg38.wgEncodeGencodePdbV38.transcriptId dupeOk + hg38.wgEncodeGencodeAttrsV38.transcriptId minCheck=0.015 + +identifier wgEncodeGencodePubMedV38 +"Link together Gencode Pubmed table with Attributes table" + hg38.wgEncodeGencodePubMedV38.transcriptId dupeOk + hg38.wgEncodeGencodeAttrsV38.transcriptId minCheck=0.63 + +identifier wgEncodeGencodeRefSeqV38 +"Link together Gencode RefSeq table with Attributes table" + hg38.wgEncodeGencodeRefSeqV38.transcriptId dupeOk + hg38.wgEncodeGencodeAttrsV38.transcriptId minCheck=0.05 + +identifier wgEncodeGencodeRefSeqToRefGeneV38 +"Link together Gencode RefSeq table with refGene track" + hg38.wgEncodeGencodeRefSeqV38.rnaAcc dupeOk chopAfter=. + hg38.refGene.name minCheck=0.77 + +identifier wgEncodeGencodeTagV38 +"Link together Gencode Tag table with Attributes table" + hg38.wgEncodeGencodeTagV38.transcriptId dupeOk + hg38.wgEncodeGencodeAttrsV38.transcriptId minCheck=0.36 + +identifier wgEncodeGencodeTranscriptSourceV38 +"Link together Gencode Transcript Source table with Attributes table" + hg38.wgEncodeGencodeTranscriptSourceV38.transcriptId + hg38.wgEncodeGencodeAttrsV38.transcriptId + +identifier wgEncodeGencodeTranscriptSupportV38 +"Link together Gencode Transcript Support table with Attributes table" + hg38.wgEncodeGencodeTranscriptSupportV38.transcriptId dupeOk + hg38.wgEncodeGencodeAttrsV38.transcriptId minCheck=0.04 + +identifier wgEncodeGencodeTranscriptionSupportLevelV38 +"Link together Gencode Transcription Support Level table with Attributes table" + hg38.wgEncodeGencodeTranscriptionSupportLevelV38.transcriptId dupeOk + hg38.wgEncodeGencodeAttrsV38.transcriptId minCheck=0.30 + +identifier wgEncodeGencodeUniProtV38 +"Link together Gencode UniProt Support table with Attributes table" + hg38.wgEncodeGencodeUniProtV38.transcriptId dupeOk + hg38.wgEncodeGencodeAttrsV38.transcriptId minCheck=0.35 + +identifier wgEncodeGencodeAnnotationRemarkV38 +"Link together Gencode Annotation Remark table with Attributes table" + hg38.wgEncodeGencodeAnnotationRemarkV38.transcriptId dupeOk + hg38.wgEncodeGencodeAttrsV38.transcriptId minCheck=0.10 + +identifier wgEncodeGencodeEntrezGeneV38 +"Link together Gencode UniProt Support table with Attributes table" + hg38.wgEncodeGencodeEntrezGeneV38.transcriptId dupeOk + hg38.wgEncodeGencodeEntrezGeneV38.transcriptId minCheck=0.35 + +identifier wgEncodeGencodeExonSupportV38 +"Link together Gencode Exon Support table with Attributes table" + hg38.wgEncodeGencodeExonSupportV38.transcriptId dupeOk + hg38.wgEncodeGencodeAttrsV38.transcriptId minCheck=0.80 + +# end Gencode V38 + # 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 @@ -4262,126 +4357,119 @@ hg19.wgEncodeGencodeUniProtV37lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV37lift37.transcriptId minCheck=0.35 identifier wgEncodeGencodeAnnotationRemarkV37lift37 "Link together Gencode Annotation Remark table with Attributes table" hg19.wgEncodeGencodeAnnotationRemarkV37lift37.transcriptId dupeOk hg19.wgEncodeGencodeAttrsV37lift37.transcriptId minCheck=0.10 identifier wgEncodeGencodeEntrezGeneV37lift37 "Link together Gencode UniProt Support table with Attributes table" hg19.wgEncodeGencodeEntrezGeneV37lift37.transcriptId dupeOk hg19.wgEncodeGencodeEntrezGeneV37lift37.transcriptId minCheck=0.35 # end Gencode V37lift37 -# begin Gencode V38 +# begin Gencode V38lift37 # gencode genePred tables with no associations -# wgEncodeGencodePolyaV38 -# wgEncodeGencode2wayConsPseudoV38 +# wgEncodeGencodePolyaV38lift37 +# wgEncodeGencode2wayConsPseudoV38lift37 -# gencode genePred tables with joining through wgEncodeGencodeAttrsV38 -identifier wgEncodeGencodeBasicAttrsV38 +# gencode genePred tables with joining through wgEncodeGencodeAttrsV38lift37 +identifier wgEncodeGencodeBasicAttrsV38lift37 "Link together Gencode Basic Table with Attributes table" - hg38.wgEncodeGencodeAttrsV38.transcriptId - hg38.wgEncodeGencodeBasicV38.name + hg19.wgEncodeGencodeAttrsV38lift37.transcriptId + hg19.wgEncodeGencodeBasicV38lift37.name -identifier wgEncodeGencodeCompAttrsV38 +identifier wgEncodeGencodeCompAttrsV38lift37 "Link together Gencode Comprehensive Table with Attributes table" - hg38.wgEncodeGencodeAttrsV38.transcriptId - hg38.wgEncodeGencodeCompV38.name + hg19.wgEncodeGencodeAttrsV38lift37.transcriptId + hg19.wgEncodeGencodeCompV38lift37.name -identifier wgEncodeGencodePseudoGeneAttrsV38 +identifier wgEncodeGencodePseudoGeneAttrsV38lift37 "Link together Gencode PseudoGene Table with Attributes table" - hg38.wgEncodeGencodeAttrsV38.transcriptId - hg38.wgEncodeGencodePseudoGeneV38.name + hg19.wgEncodeGencodeAttrsV38lift37.transcriptId + hg19.wgEncodeGencodePseudoGeneV38lift37.name -# gencode association tables (joined through wgEncodeGencodeAttrsV38) -identifier wgEncodeGencodeGeneSourceV38 +# gencode association tables (joined through wgEncodeGencodeAttrsV38lift37) +identifier wgEncodeGencodeGeneSourceV38lift37 "Link together Gencode Gene Source table with Attributes table" - hg38.wgEncodeGencodeGeneSourceV38.geneId - hg38.wgEncodeGencodeAttrsV38.geneId + hg19.wgEncodeGencodeGeneSourceV38lift37.geneId + hg19.wgEncodeGencodeAttrsV38lift37.geneId -identifier wgEncodeGencodeGeneSymbolV38 +identifier wgEncodeGencodeGeneSymbolV38lift37 "Link together Gencode gene symbol table with Attributes table" - hg38.wgEncodeGencodeGeneSymbolV38.transcriptId dupeOk - hg38.wgEncodeGencodeAttrsV38.transcriptId minCheck=0.20 + hg19.wgEncodeGencodeGeneSymbolV38lift37.transcriptId dupeOk + hg19.wgEncodeGencodeAttrsV38lift37.transcriptId minCheck=0.20 -identifier wgEncodeGencodePdbV38 +identifier wgEncodeGencodePdbV38lift37 "Link together Gencode Pdb table with Attributes table" - hg38.wgEncodeGencodePdbV38.transcriptId dupeOk - hg38.wgEncodeGencodeAttrsV38.transcriptId minCheck=0.015 + hg19.wgEncodeGencodePdbV38lift37.transcriptId dupeOk + hg19.wgEncodeGencodeAttrsV38lift37.transcriptId minCheck=0.015 -identifier wgEncodeGencodePubMedV38 +identifier wgEncodeGencodePubMedV38lift37 "Link together Gencode Pubmed table with Attributes table" - hg38.wgEncodeGencodePubMedV38.transcriptId dupeOk - hg38.wgEncodeGencodeAttrsV38.transcriptId minCheck=0.63 + hg19.wgEncodeGencodePubMedV38lift37.transcriptId dupeOk + hg19.wgEncodeGencodeAttrsV38lift37.transcriptId minCheck=0.63 -identifier wgEncodeGencodeRefSeqV38 +identifier wgEncodeGencodeRefSeqV38lift37 "Link together Gencode RefSeq table with Attributes table" - hg38.wgEncodeGencodeRefSeqV38.transcriptId dupeOk - hg38.wgEncodeGencodeAttrsV38.transcriptId minCheck=0.05 + hg19.wgEncodeGencodeRefSeqV38lift37.transcriptId dupeOk + hg19.wgEncodeGencodeAttrsV38lift37.transcriptId minCheck=0.05 -identifier wgEncodeGencodeRefSeqToRefGeneV38 +identifier wgEncodeGencodeRefSeqToRefGeneV38lift37 "Link together Gencode RefSeq table with refGene track" - hg38.wgEncodeGencodeRefSeqV38.rnaAcc dupeOk chopAfter=. - hg38.refGene.name minCheck=0.77 + hg19.wgEncodeGencodeRefSeqV38lift37.rnaAcc dupeOk chopAfter=. + hg19.refGene.name minCheck=0.77 -identifier wgEncodeGencodeTagV38 +identifier wgEncodeGencodeTagV38lift37 "Link together Gencode Tag table with Attributes table" - hg38.wgEncodeGencodeTagV38.transcriptId dupeOk - hg38.wgEncodeGencodeAttrsV38.transcriptId minCheck=0.36 + hg19.wgEncodeGencodeTagV38lift37.transcriptId dupeOk + hg19.wgEncodeGencodeAttrsV38lift37.transcriptId minCheck=0.36 -identifier wgEncodeGencodeTranscriptSourceV38 +identifier wgEncodeGencodeTranscriptSourceV38lift37 "Link together Gencode Transcript Source table with Attributes table" - hg38.wgEncodeGencodeTranscriptSourceV38.transcriptId - hg38.wgEncodeGencodeAttrsV38.transcriptId + hg19.wgEncodeGencodeTranscriptSourceV38lift37.transcriptId + hg19.wgEncodeGencodeAttrsV38lift37.transcriptId -identifier wgEncodeGencodeTranscriptSupportV38 +identifier wgEncodeGencodeTranscriptSupportV38lift37 "Link together Gencode Transcript Support table with Attributes table" - hg38.wgEncodeGencodeTranscriptSupportV38.transcriptId dupeOk - hg38.wgEncodeGencodeAttrsV38.transcriptId minCheck=0.04 + hg19.wgEncodeGencodeTranscriptSupportV38lift37.transcriptId dupeOk + hg19.wgEncodeGencodeAttrsV38lift37.transcriptId minCheck=0.04 -identifier wgEncodeGencodeTranscriptionSupportLevelV38 +identifier wgEncodeGencodeTranscriptionSupportLevelV38lift37 "Link together Gencode Transcription Support Level table with Attributes table" - hg38.wgEncodeGencodeTranscriptionSupportLevelV38.transcriptId dupeOk - hg38.wgEncodeGencodeAttrsV38.transcriptId minCheck=0.30 + hg19.wgEncodeGencodeTranscriptionSupportLevelV38lift37.transcriptId dupeOk + hg19.wgEncodeGencodeAttrsV38lift37.transcriptId minCheck=0.30 -identifier wgEncodeGencodeUniProtV38 +identifier wgEncodeGencodeUniProtV38lift37 "Link together Gencode UniProt Support table with Attributes table" - hg38.wgEncodeGencodeUniProtV38.transcriptId dupeOk - hg38.wgEncodeGencodeAttrsV38.transcriptId minCheck=0.35 + hg19.wgEncodeGencodeUniProtV38lift37.transcriptId dupeOk + hg19.wgEncodeGencodeAttrsV38lift37.transcriptId minCheck=0.35 -identifier wgEncodeGencodeAnnotationRemarkV38 +identifier wgEncodeGencodeAnnotationRemarkV38lift37 "Link together Gencode Annotation Remark table with Attributes table" - hg38.wgEncodeGencodeAnnotationRemarkV38.transcriptId dupeOk - hg38.wgEncodeGencodeAttrsV38.transcriptId minCheck=0.10 + hg19.wgEncodeGencodeAnnotationRemarkV38lift37.transcriptId dupeOk + hg19.wgEncodeGencodeAttrsV38lift37.transcriptId minCheck=0.10 -identifier wgEncodeGencodeEntrezGeneV38 +identifier wgEncodeGencodeEntrezGeneV38lift37 "Link together Gencode UniProt Support table with Attributes table" - hg38.wgEncodeGencodeEntrezGeneV38.transcriptId dupeOk - hg38.wgEncodeGencodeEntrezGeneV38.transcriptId minCheck=0.35 - -identifier wgEncodeGencodeExonSupportV38 -"Link together Gencode Exon Support table with Attributes table" - hg38.wgEncodeGencodeExonSupportV38.transcriptId dupeOk - hg38.wgEncodeGencodeAttrsV38.transcriptId minCheck=0.80 - -# end Gencode V38 - + hg19.wgEncodeGencodeEntrezGeneV38lift37.transcriptId dupeOk + hg19.wgEncodeGencodeEntrezGeneV38lift37.transcriptId minCheck=0.35 +# end Gencode V38lift37 # begin Gencode VM2 # gencode genepreds with no associations # wgEncodeGencodePolyaVM2 # wgEncodeGencode2wayConsPseudoVM2 # gencode genepreds with joining through wgEncodeGencodeAttrsVM2 identifier wgEncodeGencodeBasicAttrsVM2 "Link together Gencode Basic Table with Attributes table" mm10.wgEncodeGencodeAttrsVM2.transcriptId mm10.wgEncodeGencodeBasicVM2.name identifier wgEncodeGencodeCompAttrsVM2 "Link together Gencode Comprehensive Table with Attributes table"