2cb2236b2ebb81e95c173a35ec590f5a086b86d0 lrnassar Thu Mar 26 17:32:56 2026 -0700 Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> diff --git src/hg/makeDb/trackDb/relatedTracks.ra src/hg/makeDb/trackDb/relatedTracks.ra index 973c22d1151..fe4044364e6 100644 --- src/hg/makeDb/trackDb/relatedTracks.ra +++ src/hg/makeDb/trackDb/relatedTracks.ra @@ -29,30 +29,35 @@ 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 hg38 phasedVars varFreqs The variant frequencies track contains projects where variant frequencies, aka allele frequencies, are publicly available. hg38 varFreqs phasedVars The phased variants track contains projects that provide haplotype-phased genotypes/variants. +hg38 wgEncodeReg4 wgEncodeReg ENCODE4 update of ENCODE3 Regulation +hg38 wgEncodeReg wgEncodeReg4 ENCODE4 update of ENCODE3 Regulation +hg38 wgEncodeReg4 cCREs Related ENCODE4 cCRE annotations +hg38 cCREs wgEncodeReg4 Related ENCODE4 regulation data + # 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 @@ -64,15 +69,21 @@ 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. hg19 constraintSuper gnomadPLI Predicted constraint metrics from gnomAD hg19 gnomadPLI constraintSuper Container track of various constraint scores # mm39: mm39 knownGene knownGeneArchive View previous versions of GENCODE Genes mm39 knownGeneArchive knownGene View the latest GENCODE Genes version + +# mm10 ENCODE4 Regulation: +mm10 encode4Reg encode3Reg ENCODE4 update of ENCODE3 Regulation +mm10 encode3Reg encode4Reg ENCODE4 update of ENCODE3 Regulation +mm10 encode4Reg cCREs Related ENCODE4 cCRE annotations +mm10 cCREs encode4Reg Related ENCODE4 regulation data