9f975b6fc35649e71cfbf7c63bb8cd06c2244598 max Tue May 2 02:59:23 2023 -0700 adding more details to refseq docs page, and preparing the removal of the hg19-specific refseq docs page, refs #31118 diff --git src/hg/makeDb/trackDb/relatedTracks.ra src/hg/makeDb/trackDb/relatedTracks.ra index 17b2bf4..8e61792 100644 --- src/hg/makeDb/trackDb/relatedTracks.ra +++ src/hg/makeDb/trackDb/relatedTracks.ra @@ -1,55 +1,58 @@ # A space delimited file of track relatedness, format: # ucscDb track trackLinkingTo reason # hg38: hg38 miRnaAtlas nonCodingRNAs View associated precursor miRnas hg38 nonCodingRNAs miRnaAtlas View expression of cleaved miRnas hg38 caddSuper gnomad View associated variants hg38 gnomad caddSuper View CADD scores for this variant and region hg38 revel liftHg38 Revel is based on hg19 and lifted to hg38. liftOver "chain" alignment from hg19 to hg38 hg38 liftHg38 revel Revel scores were lifted using UCSC liftOver chains from hg38 hg38 revel caddSuper CADD, a similar deleteriousness score, and not used as an input by REVEL hg38 caddSuper revel REVEL, a similar deleteriousness score hg38 liftHg19 grcIncidentDb GRC Incident database, to explore reasons why the assembly was changed hg38 grcIncidentDb liftHg19 LiftOver for hg38, explores how incident regions aligned between human assemblies hg38 ReMap liftHg19 NCBI ReMap, even though it has the same name, is a liftOver-like hg19/hg38 alignment, and unrelated to the ReMap database hg38 liftHg19 ReMap ReMap, even though it has the same name, is a database of transcription factor binding sites, unrelated to NCBI ReMap hg38 ReMap jaspar JASPAR is a database of predicted TF binding sites, based on short DNA matches. Unlike ReMap, the data is purely computational. hg38 jaspar ReMap ReMap is a database of TF binding sites inferred from ChIP-Seq Data. Unlike JASPAR predictions, these sites are supported by functional assay hg38 problematic mappability The mappability track contains regions where short sequencing reads are hard to align hg38 mappability problematic The problematic regions track contains various gene clusters and the ENCODE blacklist hg38 problematic grcIncidentDb The GRC (Genome Reference Consortium) incidents track contains regions that were flagged by the group that puts together the genome hg38 grcIncidentDb problematic The problematic regions track lists unusual regions and the ones that often lead to artefacts when aligning reads to the reference genome # hg19: hg19 caddSuper gnomad View associated variants hg19 gnomad caddSuper View CADD scores for this variant and region hg19 decipherHaploIns gnomadPLI Compare haploinsufficiency metrics as defined by gnomAD hg19 gnomadPLI decipherHaploIns Compare constraint metrics as defined by DECIPHER hg19 revel caddSuper CADD, a similar deleteriousness score, and not used as an input by REVEL hg19 caddSuper revel REVEL, a similar deleteriousness score hg19 liftHg38 grcIncidentDb GRC Incident database, to explore reasons why the assembly was changed hg19 grcIncidentDb liftHg38 LiftOver alignments between hg38 and hg38 to explore how the GRC incident assembly changes affect whole-genome alignments between hg19 and hg38 used for lifting data from hg19 hg19 fixSeqLiftOverPsl liftHg38 Investigate how patches affect the whole-genome alignment used for liftOver hg19 liftHg38 fixSeqLiftOverPsl Investigate how assembly patches affect the liftOver alignment hg19 liftHg38 hg38ContigDiff Hg38 Diff shows contigs that were changed from hg19 to hg38 hg19 hg38ContigDiff liftHg38 Investigate how contig changes affect the liftOver alignments hg19 jaspar ReMap ReMap is a database of TF binding sites inferred from ChIP-Seq Data. Unlike JASPAR predictions, these sites are supported by functional assay hg19 ReMap jaspar JASPAR is a database of predicted TF binding sites, based on short DNA matches. Unlike ReMap, the data is purely computational. hg19 ReMap liftHg38 NCBI ReMap, even though it has the same name, is a liftOver-like hg19/hg38 alignment, and unrelated to the ReMap database hg19 liftHg38 ReMap ReMap, even though it has the same name, is a database of transcription factor binding sites, unrelated to NCBI ReMap + +hg19 refSeqComposite pseudoYale60 NCBI RefSeq Curated and RefSeq Other contains pseudogenes, but the Yale annotation should be more comprehensive for this transcript type +hg19 pseudoYale60 refSeqComposite NCBI RefSeq Curated and RefSeq Other also contain some transcribed and untranscribed pseudogenes, respectively.