Track Data Hubs
 

Track data hubs are collections of external tracks that can be added to the UCSC Genome Browser. Click Connect to attach a hub and redirect to the assembly gateway page. Hub tracks will then show up in the hub's own blue bar track group under the browser graphic. For more information, including where to host your track hub, see our User's Guide.

Track Hubs are created and maintained by external sources. UCSC is not responsible for their content.

The list below can be filtered on words in the hub description pages or by assemblies.
Search terms: Assembly:
Display Hub Name Description AssembliesClick to connect and browse directly
ABC of cellular microRNAome Advanced BarChart configuration of cellular microRNAome. Evaluation of >20 billion small RNA-seq reads from 196 primary cell types (+plasma, +platelets) across 175 main studies. hg38
ALFA Hub NCBI's Allele Frequency Aggregator (ALFA) allele frequency for variants in dbGaP studies. hg19, hg38
Bird Alignment (363 species) Bird Alignment (363 species) [+] Gallus_gallus, Acanthisitta_chloris...
Blueprint Hub Blueprint Epigenomics Data Hub hg38
BrainEpigenomeHub DNA methylation, chromatin accessibility, and gene expression data from NeuN flow-sorted human brain samples hg19
BRCAExchange BRCAExchange annotated BRCA1/2 variants hg19, hg38
Breast Cancer Epigenomics Track Hub Breast Cancer Epigenomics Track Hub hg19
Breast Cancer lncRNA Breast Cancer lncRNA PMID 26236012 hg19
C_elegans_isolates C. elegans wild isolate assembly hub [+] CB4856Princeton_JR-contig...
CADD CADD Track for v1.3 to v1.7 hg19, hg38
Cancer Genomics Tracks TCGA and ICGC Cancer Mutations, TCGA Expression, Immune Epitopes Database (IEDB), Cancer Immunity Peptides Database, Dienstmann Variant/Cancer database, CIVIC, MyCancerGenome.org, OncoKB hg19
CCGP The California Conservation Genomics Project (CCGP) assemblies [+] GCA_026170555.1, GCA_026170545.1...
CEMT (CEEHRC) Epigenomic Data tracks from BCGSC, Vancouver, B.C. hg38, hg19
CESAR Gene Mappings Human Exons mapped by CESAR [+] bosTau7, ailMel1, allMis1, anoCar2, calJac3...
ChIP-seq data track HUBs from MSC cells from GSE79815 ChIP-seq data from the publication "Epigenetic plasticity drives adipogenic and osteogenic differentiation of marrow-derived mesenchymal stem cells" (10.1074/jbc.M116.736538) from GEO record GSE79815 mm9
Coloc segments Colocalized segments of human genome for Roadmap cell types hg19
Cotney Lab Human Craniofacial Epigenomics Human Embryonic Craniofacial Tissue Epigenomic Data and Chromatin State Segmentations from the Cotney Lab at CHOP hg19, mm9, mm10, hg38
Cotney Lab Human Embryonic Heart Hub Human Embryonic Heart Tissue Epigenomic and Transcriptomic Data from the Cotney Lab at CHOP hg19, hg38
COVID-19 Gene Annotation GENCODE annotation of COVID-19 associated genes hg38
crisprware Cas9 and Cas12A crisprware Cas9 and Cas12A hg38, ce11, rn7, danRer11, dm6, mm39
Croc and Bird Hub ERROR: Couldn't open https://s3-us-west-2.amazonaws.com/croc-paper-hub/hub.txt Debug Help [+] allMis2, Anc00, Anc01, Anc02, Anc03, Anc04, Anc06...
DANIO-CODE Track Hub DANIO-CODE: Central repository for zebrafish genomic datasets danRer10, danRer11
DASHR small ncRNA Hub DASHR Human small non-coding RNA data hg19
DASHR v2.0 Hub DASHR v2.0 Human small non-coding RNA data hub hg19, hg38
dbRIP_Hub "dbRIP: Database of Polymorphic and Species-specific Retrotransposons in Humans" hg19, hg38
dbVar Hub NCBI's database of human genomic Structural Variation -- large variants >50 bp hg19, hg38
Dfam database of TE families and annotations Dfam database of Transposable Element families and genome annotations hg38
Digital genomic footprinting (Vierstra et al., 2020) Digital genomic footprinting from 243 cell & tissue types hg38
ENCODE Analysis Hub ENCODE Integrative Analysis Data Hub hg19
ENCODE DNA Trackhub ENCODE Trackhub for DNA-based assays hg19, hg38, mm10
ENCODE integrative Trackhub ENCODE Trackhub for integrative results hg38, mm10
ENCODE RNA Trackhub ENCODE Trackhub for RNA-based assays hg19, hg38, mm10
ENIGMA BRCA1/BRCA2 specs 1.1.0 ENIGMA BRCA1/BRCA2 Panel Specifications of ACMG/AMP Guidelines version 1.1.0 hg38, hg19
Ensembl Regulatory Build Evidence summaries and provisional results for the new Ensembl Regulatory Build hg38, hg19, mm10
EPD Viewer Hub Promoter specific experimental data and TSS annotation from the EPD database [+] hg19, hg38, mm9, mm10, danRer7, rheMac8, galGal5, rn6...
EPIraction EPIraction - an atlas of candidate enhancer-gene interactions in human tissues and cell lines. hg38
ExonEnhancers Mouren et al. Exonic enhancers are a widespread class of dual-function regulatory elements. (in prep.) hg38, hg19, mm39, dm6, GCF_000001735.3
Exp/Meth VNTR hub Association of VNTRs with Expression and Methylation in GTEx, PCGC and PPMI hg19, hg38
EyeBrowse Eye tissue specific genes and markers, derived from NEIBank and other sources [+] hg19, bosTau6, canFam2, cavPor3, danRer6, danRer7...
FaceBase Hub Comprehensive craniofacial research data from FaceBase.org mm9, mm10, hg18, hg19
FANTOM5 RIKEN FANTOM5 Phase1 and Phase2 data hg38, mm10, hg19, mm9, canFam3, rn6, rheMac8, galGal5
FANTOM5 CAGE RECLU DATA RIKEN FANTOM5 CAGE clusters by RECLU hg19, hg18
Forebrain Enhancer Tracks Predicted Forebrain Enhancers for Human Genome hg19
FUNCODE scores FUNCODE scores: Functional conservation between human and mouse from ENCODE consortium hg38, mm10
GENCODE Annotation Updates Updates to GENCODE manual annotation since last release hg38, mm39, mm10
GeneCards ncRNAs An integrated compendium of ncRNA genes in GeneCards hg38
GeneHancer GeneHancer: genome-wide integration of regulatory elements and target genes in GeneCards hg38, hg19
Golden Hamster genome Genome assembly of Golden Hamster(Mesocricetus auratus) from Siomi lab MesAur2.0
GTEx Analysis Hub Genotype Tissue Expression (GTEx) Project Analysis Hub hg19, hg38
GTEx RNA-seq Signal Hub RNA-seq read coverage in 53 tissues from GTEx V6 (7572 samples) hg19, hg38
Hub for genetrek.pasteur.fr website data Hub gathering data from the Human Genetics and Cognitive Function lab at Institut Pasteur (see http://genetrek.pasteur.fr) hg38
Human cellular microRNAome microRNA RNA-seq based data from 46 primary cell types and 42 cancer or immortalized cell lines. hg38
Human cellular microRNAome barCharts Evaluation of >10 billion small RNA-seq reads from 78 primary cell types and 42 cancer or immortalized cell lines from 3 main studies. hg38
Human Global Reference Genomes Human Global Reference Genome assembly hub [+] GCA_003601015.1_HG03807_prelim_1.0...
human p53 Binding And Expression Resource (BAER) hub ERROR: Couldn't open https://orio.niehs.nih.gov/ucscview/nguyen/p53BAER/hub.txt Debug Help hg19
IDEAS roadmap 20states Roadmap Epigenomics 20 state genome segmentation using the IDEAS algorithm hg19
IMPACT regulatory element activity Cell-type-specific regulatory element activity profiles across 707 unique combinations of transcription factor-cell type pairs. IMPACT predicts the epigenetic regulatory activity related to a particular transcription factor in a given cell type. hg19
JASPAR TFBS ERROR: Couldn't open http://expdata.cmmt.ubc.ca/JASPAR/UCSC_tracks/hub.txt Debug Help [+] hg19, hg38, ce10, ce11, ci3, dm6, sacCer3, danRer10...
LIBD Human DLPFC Development RNAseq data across human brain development by age group from LIBD hg19
LNCipedia 5.2 LNCipedia 5.2 - A comprehensive compendium of human long non-coding RNAs hg19, hg38
Mammal and Bird Alignment (605 species) Mammal and Bird Alignment (605 species) [+] Homo_sapiens, Gallus_gallus...
MethBase (Legacy) MethBase: 605 DNA Methylation profiles reprocessed from NCBI SRA [+] hg38, canFam3, panTro2, hg18, rheMac8, danRer11...
MethBase2 Over 15,000 high quality full-genome DNA methylation profiles. [+] hg38, ailMel1, apiMel2, bosTau9, calMil1, canFam6...
MGI Alleles and Phenotypes Allele's and Phenotypes from the Mouse Genome Informatics (MGI) consortium mm10
mm9.SMC1.ChIAPET Cohesin(Smc1)-associated chromatin interactions in murine embryonic stem cells mm9
Mouse strain assemblies Assembly and alignment data for 16 different mouse strains plus rat. [+] mm10, rn6, 129S1_SvImJ, WSB_EiJ, SPRET_EiJ, AKR_J...
MutScore Variant Pathogenicity ERROR: Host mutscore-ucsc.iob.ch not found --> Name or service not known netConnect() failed Couldn't open https://mutscore-ucsc.iob.ch/hub.txt Debug Help hg38, hg19
ORF Predictions RNA-Seq, Ribo_Seq, and ORF Predictions wuhCor1
Peptide evidences CNIO Peptides detected from a re-analysis of multiple experiments and databases hg38, hg19
Peterhof_yeasts Peterhof_yeast [+] sacCer3, 1B_D1606_spades...
PhyloCSF Evolutionary protein-coding potential as measured by PhyloCSF [+] hg19, hg38, mm10, mm39, galGal4, galGal6, dm6, ce11...
PhyloCSF++ Evolutionary protein-coding potential as measured by PhyloCSF++ rn6, fr3, gasAcu1, tarSyr2, sacCer3
Polytract Repeats Very Short Tandem Repeats (MNR/DNR/TNR) hg38, mm10, rn6, dm6
Predominant PAS and predominant hexamers Predominant polyA sites and predominant hexamers hg38, hg19
Primate x4 NeuroDiff and Human CRISPRa RNAseq coverage tracks from 4 Primate neuro-differentiation assays and a human CRISPRa assay hg19, panTro4, ponAbe2, rheMac8
Principal Splice Isoforms APPRIS Selects a single CDS variant for each gene as the 'PRINCIPAL' isoform based on the range of protein features. [+] hg38, hg19, mm10, danRer10, rn6, susScr3, panTro4, dm6...
Promoterome CAGE and nucleosome positioning Zebrafish promoterome based on Haberle et al. and Nepal et al. danRer7
PsychENCODE MPRA Hub PsychENCODE MPRA Hub hg38
Purple sea star Assembly Hub This is the Assembly Hub of the purple sea star (Pisaster ochraceus, assembly 12Jun2017_28pcJ) 12Jun2017_28pcJ
RefSeqFE Hub NCBI RefSeq Functional Elements interactions and features GCA_009914755.4, hg19, hg38, hs1, mm10, mm39
refTSS refTSS hg38, mm10, mm39
ReMap 2018 Regulatory Atlas ReMap 2018: An atlas of regulatory regions from an integrative analysis of Human DNA-binding sequencing experiments. Go to ReMap for more info. Pubmed link. hg38
ReMap 2020 Regulatory Atlas ReMap 2020: An atlas of regulatory regions from an integrative analysis of Human and Arabidopsis thaliana DNA-binding sequencing experiments. Go to ReMap for more info. hg38, araTha1
ReMap 2022 Regulatory Atlas ReMap 2022: A database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments Go to ReMap2022 for more info. mm10, mm39, hg38, hg19, dm6, araTha1
rfam12_ncRNA Rfam 12.0 non-coding RNA annotation hg38, mm10, ce10, galGal4, ci2, danRer7, dm6, sacCer3
Roadmap Epigenomics Data Complete Collection at Wash U VizHub Roadmap Epigenomics Human Epigenome Atlas Data Complete Collection, VizHub at Washington University in St. Louis hg19, hg38
Roadmap Epigenomics Integrative Analysis Hub Roadmap Epigenomics Integrative Analysis Hub at Washington University in St. Louis hg19
Seq-data on mm9 NS5 cells Set of sequencing data on mm9 NS5 cells mm9
SIHUMI simplified human intestinal microbiota HUB [+] bact, bifi, blautia, anaero, ery, clostri, lacto...
singing mouse genome hub This is the genome hub for Alston's singing mouse (Scotinomys teguina) steguina
Single Cell ATAC-seq Developing Cranial Motor Neurons Single Cell ATAC-seq bigWig Signal Tracks from Mouse Brain Motor Neurons mm10
Splice Site Usage Hub Splice Site Usage Values Calculated for 19 ENCODE Cell Lines from RNA-seq hg19
Spotted Lanternfly Assembly Hub This is the Assembly Hub of the spotted lanternfly (Lycorma delicatula) with assembly for both haplotype 1 (SLF_Hap1) and haplotype 2 (SLF_Hap2). SLF_Hap1, SLF_Hap2
sunflower_sea_star Pycnopodia helianthoides (sunflower sea star) sunflower_sea_star
Synonymous Constraint Synonymous Constraint Elements and Synonymous Acceleration Elements in protein-coding regions hg19, hg38, wuhCor1
T2T Macaque Hub T2T Macaque Hub GCA_049350105.2, GCF_037993035.2
T_cell_ATAC_ChIP_Pipkin T cell ATACseq ChIPseq assembly by Pipkin lab mm10
TCGA Cancer Effect Size Tracks Cancer Effect Size tracks - 20 TCGA Cancer Types hg38
TOBIAS footprint prediction Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal hg38, mm10
Translation Initiation Sites (TIS) Translation Initiation Sites (TIS) track hg19
UCSC Repeat Browser 2020 Update Human Repeat consensuses annotated with lifted tracks hg38reps, hg19, hg38
Ultraconserved Elements Ultra conserved Elements in the Human Genome. Science 304(5675) pp.1321-1325 (2004) hg19
Umap and Bismap mappability Uniquely mappable regions of genome and methylome hg38, hg19, mm9, mm10
UMassMed ZHub UMassMed H3K4me3 ChIP-seq data for Autistic brains hg19
UniBind 2018 Hub UniBind: A map of direct TF-DNA interactions from ChIP-seq and TF binding profiles hg38
UniBind 2021 permissive Hub UniBind 2021 hub for permissive direct TF-DNA interactions [+] hg38, mm10, ce11, dm6, danRer11, spo2, sacCer3, rn6...
UniBind 2021 Robust Hub UniBind 2021 hub for robust direct TF-DNA interactions [+] hg38, mm10, ce11, dm6, danRer11, sacCer3, rn6, araTha1...
UniProt Features UniProtKB reviewed protein features mapped to the Ensembl genome assembly. hg38
UniversalEPI ENCODE Hi-C predictions made by UniversalEPI using 157 ATAC-seq profiles from ENCODE hg38
Vista Enhancers Vista Browser Track Hub hg19, mm9, mm10
Wasp spider hub This is the assembly hub of the wasp spider (Argiope bruennichi) argiope
ZebrafishGenomics Burgess Lab Zebrafish Genomic Resources danRer11, danRer10, danRer7
ABC of cellular microRNAome Advanced BarChart configuration of cellular microRNAome. Evaluation of >20 billion small RNA-seq reads from 196 primary cell types (+plasma, +platelets) across 175 main studies. hg38
ALFA Hub NCBI's Allele Frequency Aggregator (ALFA) allele frequency for variants in dbGaP studies. hg19, hg38
Bird Alignment (363 species) Bird Alignment (363 species) [+] Gallus_gallus, Acanthisitta_chloris...
Blueprint Hub Blueprint Epigenomics Data Hub hg38
BrainEpigenomeHub DNA methylation, chromatin accessibility, and gene expression data from NeuN flow-sorted human brain samples hg19
BRCAExchange BRCAExchange annotated BRCA1/2 variants hg19, hg38
Breast Cancer Epigenomics Track Hub Breast Cancer Epigenomics Track Hub hg19
Breast Cancer lncRNA Breast Cancer lncRNA PMID 26236012 hg19
C_elegans_isolates C. elegans wild isolate assembly hub [+] CB4856Princeton_JR-contig...
CADD CADD Track for v1.3 to v1.7 hg19, hg38
Cancer Genomics Tracks TCGA and ICGC Cancer Mutations, TCGA Expression, Immune Epitopes Database (IEDB), Cancer Immunity Peptides Database, Dienstmann Variant/Cancer database, CIVIC, MyCancerGenome.org, OncoKB hg19
CCGP The California Conservation Genomics Project (CCGP) assemblies [+] GCA_026170555.1, GCA_026170545.1...
CEMT (CEEHRC) Epigenomic Data tracks from BCGSC, Vancouver, B.C. hg38, hg19
CESAR Gene Mappings Human Exons mapped by CESAR [+] bosTau7, ailMel1, allMis1, anoCar2, calJac3...
ChIP-seq data track HUBs from MSC cells from GSE79815 ChIP-seq data from the publication "Epigenetic plasticity drives adipogenic and osteogenic differentiation of marrow-derived mesenchymal stem cells" (10.1074/jbc.M116.736538) from GEO record GSE79815 mm9
Coloc segments Colocalized segments of human genome for Roadmap cell types hg19
Cotney Lab Human Craniofacial Epigenomics Human Embryonic Craniofacial Tissue Epigenomic Data and Chromatin State Segmentations from the Cotney Lab at CHOP hg19, mm9, mm10, hg38
Cotney Lab Human Embryonic Heart Hub Human Embryonic Heart Tissue Epigenomic and Transcriptomic Data from the Cotney Lab at CHOP hg19, hg38
COVID-19 Gene Annotation GENCODE annotation of COVID-19 associated genes hg38
crisprware Cas9 and Cas12A crisprware Cas9 and Cas12A hg38, ce11, rn7, danRer11, dm6, mm39
Croc and Bird Hub ERROR: Couldn't open https://s3-us-west-2.amazonaws.com/croc-paper-hub/hub.txt Debug Help [+] allMis2, Anc00, Anc01, Anc02, Anc03, Anc04, Anc06...
DANIO-CODE Track Hub DANIO-CODE: Central repository for zebrafish genomic datasets danRer10, danRer11
DASHR small ncRNA Hub DASHR Human small non-coding RNA data hg19
DASHR v2.0 Hub DASHR v2.0 Human small non-coding RNA data hub hg19, hg38
dbRIP_Hub "dbRIP: Database of Polymorphic and Species-specific Retrotransposons in Humans" hg19, hg38
dbVar Hub NCBI's database of human genomic Structural Variation -- large variants >50 bp hg19, hg38
Dfam database of TE families and annotations Dfam database of Transposable Element families and genome annotations hg38
Digital genomic footprinting (Vierstra et al., 2020) Digital genomic footprinting from 243 cell & tissue types hg38
ENCODE Analysis Hub ENCODE Integrative Analysis Data Hub hg19
ENCODE DNA Trackhub ENCODE Trackhub for DNA-based assays hg19, hg38, mm10
ENCODE integrative Trackhub ENCODE Trackhub for integrative results hg38, mm10
ENCODE RNA Trackhub ENCODE Trackhub for RNA-based assays hg19, hg38, mm10
ENIGMA BRCA1/BRCA2 specs 1.1.0 ENIGMA BRCA1/BRCA2 Panel Specifications of ACMG/AMP Guidelines version 1.1.0 hg38, hg19
Ensembl Regulatory Build Evidence summaries and provisional results for the new Ensembl Regulatory Build hg38, hg19, mm10
EPD Viewer Hub Promoter specific experimental data and TSS annotation from the EPD database [+] hg19, hg38, mm9, mm10, danRer7, rheMac8, galGal5, rn6...
EPIraction EPIraction - an atlas of candidate enhancer-gene interactions in human tissues and cell lines. hg38
ExonEnhancers Mouren et al. Exonic enhancers are a widespread class of dual-function regulatory elements. (in prep.) hg38, hg19, mm39, dm6, GCF_000001735.3
Exp/Meth VNTR hub Association of VNTRs with Expression and Methylation in GTEx, PCGC and PPMI hg19, hg38
EyeBrowse Eye tissue specific genes and markers, derived from NEIBank and other sources [+] hg19, bosTau6, canFam2, cavPor3, danRer6, danRer7...
FaceBase Hub Comprehensive craniofacial research data from FaceBase.org mm9, mm10, hg18, hg19
FANTOM5 RIKEN FANTOM5 Phase1 and Phase2 data hg38, mm10, hg19, mm9, canFam3, rn6, rheMac8, galGal5
FANTOM5 CAGE RECLU DATA RIKEN FANTOM5 CAGE clusters by RECLU hg19, hg18
Forebrain Enhancer Tracks Predicted Forebrain Enhancers for Human Genome hg19
FUNCODE scores FUNCODE scores: Functional conservation between human and mouse from ENCODE consortium hg38, mm10
GENCODE Annotation Updates Updates to GENCODE manual annotation since last release hg38, mm39, mm10
GeneCards ncRNAs An integrated compendium of ncRNA genes in GeneCards hg38
GeneHancer GeneHancer: genome-wide integration of regulatory elements and target genes in GeneCards hg38, hg19
Golden Hamster genome Genome assembly of Golden Hamster(Mesocricetus auratus) from Siomi lab MesAur2.0
GTEx Analysis Hub Genotype Tissue Expression (GTEx) Project Analysis Hub hg19, hg38
GTEx RNA-seq Signal Hub RNA-seq read coverage in 53 tissues from GTEx V6 (7572 samples) hg19, hg38
Hub for genetrek.pasteur.fr website data Hub gathering data from the Human Genetics and Cognitive Function lab at Institut Pasteur (see http://genetrek.pasteur.fr) hg38
Human cellular microRNAome microRNA RNA-seq based data from 46 primary cell types and 42 cancer or immortalized cell lines. hg38
Human cellular microRNAome barCharts Evaluation of >10 billion small RNA-seq reads from 78 primary cell types and 42 cancer or immortalized cell lines from 3 main studies. hg38
Human Global Reference Genomes Human Global Reference Genome assembly hub [+] GCA_003601015.1_HG03807_prelim_1.0...
human p53 Binding And Expression Resource (BAER) hub ERROR: Couldn't open https://orio.niehs.nih.gov/ucscview/nguyen/p53BAER/hub.txt Debug Help hg19
IDEAS roadmap 20states Roadmap Epigenomics 20 state genome segmentation using the IDEAS algorithm hg19
IMPACT regulatory element activity Cell-type-specific regulatory element activity profiles across 707 unique combinations of transcription factor-cell type pairs. IMPACT predicts the epigenetic regulatory activity related to a particular transcription factor in a given cell type. hg19
JASPAR TFBS ERROR: Couldn't open http://expdata.cmmt.ubc.ca/JASPAR/UCSC_tracks/hub.txt Debug Help [+] hg19, hg38, ce10, ce11, ci3, dm6, sacCer3, danRer10...
LIBD Human DLPFC Development RNAseq data across human brain development by age group from LIBD hg19
LNCipedia 5.2 LNCipedia 5.2 - A comprehensive compendium of human long non-coding RNAs hg19, hg38
Mammal and Bird Alignment (605 species) Mammal and Bird Alignment (605 species) [+] Homo_sapiens, Gallus_gallus...
MethBase (Legacy) MethBase: 605 DNA Methylation profiles reprocessed from NCBI SRA [+] hg38, canFam3, panTro2, hg18, rheMac8, danRer11...
MethBase2 Over 15,000 high quality full-genome DNA methylation profiles. [+] hg38, ailMel1, apiMel2, bosTau9, calMil1, canFam6...
MGI Alleles and Phenotypes Allele's and Phenotypes from the Mouse Genome Informatics (MGI) consortium mm10
mm9.SMC1.ChIAPET Cohesin(Smc1)-associated chromatin interactions in murine embryonic stem cells mm9
Mouse strain assemblies Assembly and alignment data for 16 different mouse strains plus rat. [+] mm10, rn6, 129S1_SvImJ, WSB_EiJ, SPRET_EiJ, AKR_J...
MutScore Variant Pathogenicity ERROR: Host mutscore-ucsc.iob.ch not found --> Name or service not known netConnect() failed Couldn't open https://mutscore-ucsc.iob.ch/hub.txt Debug Help hg38, hg19
ORF Predictions RNA-Seq, Ribo_Seq, and ORF Predictions wuhCor1
Peptide evidences CNIO Peptides detected from a re-analysis of multiple experiments and databases hg38, hg19
Peterhof_yeasts Peterhof_yeast [+] sacCer3, 1B_D1606_spades...
PhyloCSF Evolutionary protein-coding potential as measured by PhyloCSF [+] hg19, hg38, mm10, mm39, galGal4, galGal6, dm6, ce11...
PhyloCSF++ Evolutionary protein-coding potential as measured by PhyloCSF++ rn6, fr3, gasAcu1, tarSyr2, sacCer3
Polytract Repeats Very Short Tandem Repeats (MNR/DNR/TNR) hg38, mm10, rn6, dm6
Predominant PAS and predominant hexamers Predominant polyA sites and predominant hexamers hg38, hg19
Primate x4 NeuroDiff and Human CRISPRa RNAseq coverage tracks from 4 Primate neuro-differentiation assays and a human CRISPRa assay hg19, panTro4, ponAbe2, rheMac8
Principal Splice Isoforms APPRIS Selects a single CDS variant for each gene as the 'PRINCIPAL' isoform based on the range of protein features. [+] hg38, hg19, mm10, danRer10, rn6, susScr3, panTro4, dm6...
Promoterome CAGE and nucleosome positioning Zebrafish promoterome based on Haberle et al. and Nepal et al. danRer7
PsychENCODE MPRA Hub PsychENCODE MPRA Hub hg38
Purple sea star Assembly Hub This is the Assembly Hub of the purple sea star (Pisaster ochraceus, assembly 12Jun2017_28pcJ) 12Jun2017_28pcJ
RefSeqFE Hub NCBI RefSeq Functional Elements interactions and features GCA_009914755.4, hg19, hg38, hs1, mm10, mm39
refTSS refTSS hg38, mm10, mm39
ReMap 2018 Regulatory Atlas ReMap 2018: An atlas of regulatory regions from an integrative analysis of Human DNA-binding sequencing experiments. Go to ReMap for more info. Pubmed link. hg38
ReMap 2020 Regulatory Atlas ReMap 2020: An atlas of regulatory regions from an integrative analysis of Human and Arabidopsis thaliana DNA-binding sequencing experiments. Go to ReMap for more info. hg38, araTha1
ReMap 2022 Regulatory Atlas ReMap 2022: A database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments Go to ReMap2022 for more info. mm10, mm39, hg38, hg19, dm6, araTha1
rfam12_ncRNA Rfam 12.0 non-coding RNA annotation hg38, mm10, ce10, galGal4, ci2, danRer7, dm6, sacCer3
Roadmap Epigenomics Data Complete Collection at Wash U VizHub Roadmap Epigenomics Human Epigenome Atlas Data Complete Collection, VizHub at Washington University in St. Louis hg19, hg38
Roadmap Epigenomics Integrative Analysis Hub Roadmap Epigenomics Integrative Analysis Hub at Washington University in St. Louis hg19
Seq-data on mm9 NS5 cells Set of sequencing data on mm9 NS5 cells mm9
SIHUMI simplified human intestinal microbiota HUB [+] bact, bifi, blautia, anaero, ery, clostri, lacto...
singing mouse genome hub This is the genome hub for Alston's singing mouse (Scotinomys teguina) steguina
Single Cell ATAC-seq Developing Cranial Motor Neurons Single Cell ATAC-seq bigWig Signal Tracks from Mouse Brain Motor Neurons mm10
Splice Site Usage Hub Splice Site Usage Values Calculated for 19 ENCODE Cell Lines from RNA-seq hg19
Spotted Lanternfly Assembly Hub This is the Assembly Hub of the spotted lanternfly (Lycorma delicatula) with assembly for both haplotype 1 (SLF_Hap1) and haplotype 2 (SLF_Hap2). SLF_Hap1, SLF_Hap2
sunflower_sea_star Pycnopodia helianthoides (sunflower sea star) sunflower_sea_star
Synonymous Constraint Synonymous Constraint Elements and Synonymous Acceleration Elements in protein-coding regions hg19, hg38, wuhCor1
T2T Macaque Hub T2T Macaque Hub GCA_049350105.2, GCF_037993035.2
T_cell_ATAC_ChIP_Pipkin T cell ATACseq ChIPseq assembly by Pipkin lab mm10
TCGA Cancer Effect Size Tracks Cancer Effect Size tracks - 20 TCGA Cancer Types hg38
TOBIAS footprint prediction Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal hg38, mm10
Translation Initiation Sites (TIS) Translation Initiation Sites (TIS) track hg19
UCSC Repeat Browser 2020 Update Human Repeat consensuses annotated with lifted tracks hg38reps, hg19, hg38
Ultraconserved Elements Ultra conserved Elements in the Human Genome. Science 304(5675) pp.1321-1325 (2004) hg19
Umap and Bismap mappability Uniquely mappable regions of genome and methylome hg38, hg19, mm9, mm10
UMassMed ZHub UMassMed H3K4me3 ChIP-seq data for Autistic brains hg19
UniBind 2018 Hub UniBind: A map of direct TF-DNA interactions from ChIP-seq and TF binding profiles hg38
UniBind 2021 permissive Hub UniBind 2021 hub for permissive direct TF-DNA interactions [+] hg38, mm10, ce11, dm6, danRer11, spo2, sacCer3, rn6...
UniBind 2021 Robust Hub UniBind 2021 hub for robust direct TF-DNA interactions [+] hg38, mm10, ce11, dm6, danRer11, sacCer3, rn6, araTha1...
UniProt Features UniProtKB reviewed protein features mapped to the Ensembl genome assembly. hg38
UniversalEPI ENCODE Hi-C predictions made by UniversalEPI using 157 ATAC-seq profiles from ENCODE hg38
Vista Enhancers Vista Browser Track Hub hg19, mm9, mm10
Wasp spider hub This is the assembly hub of the wasp spider (Argiope bruennichi) argiope
ZebrafishGenomics Burgess Lab Zebrafish Genomic Resources danRer11, danRer10, danRer7

Enter hub URLs below to connect hubs. Hubs connected this way are not accessible to other users by default.

If you wish to share your hub you can create a session link. First, connect the hub and configure the tracks image as desired, then navigate to My Sessions (My Data > My Sessions). The resulting stable link can be added to publications and shared freely. We never delete them. You, as the author, also have the power to update the session contents freely. Alternatively, you may build a link with the hub URL to allow users to retain their browser configuration, connected hubs, and custom tracks.

When you are ready to share you hub more widely, see our public hub guidelines for information on submitting a new public hub.

No connected track or assembly hubs.

To connect a hub:

  • Enter its URL into the input box above and click 'Add Hub'.
  • To quickly connect a single hub URL from the Genome Browser directly, use the keyboard shortcut 'c then h'
  • Alternatively, you can go to the 'Public Hubs' tab on this page and connect one of the hubs that were submitted to us.
  • Another way to connect to hubs is via a direct connection link copied using the copy icon, shown on this page, when a hub is connected (adding &hubUrl=https://xxx to the URL).
  • You can also connect to hub by following a short link to a saved session, created though the menu 'My Data > My Sessions', if the Genome Browser had connected hubs when the session was saved.

Create your own hub

For information on making track hubs, see the following pages:
You may also contact us if you have any issues or questions on hub development.

Check a hub for errors

  Load Example URL
Use the URL bar above to check a hub for errors. This will validate the hub's configuration files, including hub.txt, genomes.txt and trackDb.txt. It will also present a hierarchical tree of tracks with any errors in red. A hub with no errors still shows the tree which can be used to explore the track hierarchy. Hub error checking will always refresh the files and never use our remote file cache (see below).

Enable Genome Browser debugging modes

These apply to all connected hubs. By default, caching is activated and track load times are not shown, but you can change these settings while developing your hub:
File caching: ON  
Current setting: Always cache contents at UCSC. This means that data access is faster, but you cannot see the effect of changes to your files on the Genome Browser for at least 5 minutes.
For custom tracks, this affects only the remote formats (bigBed, bigWig, VCF+tabix, BAM, CRAM, bigPsl, HiC, etc), not text files (BED, VCF, PSL, etc), which are stored at UCSC.
Show load times: OFF  
Current setting: Show no timing measurements.

API key

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New feature! We're excited to introduce this new hosting space.
We would love to hear your feedback — please contact us and let us know what you think!

Upload your track hub files to UCSC and view your bigBed, bigWig, BAM, VCF, and other supported files -- no need to rely on third-party hosting services such as Dropbox, Google Drive, or AWS.

Each account is allocated 10 GB of storage. While we strive to maintain uninterrupted access, please maintain your own backups. Data persistence over the long term is not guaranteed. To request additional storage space, please contact us.

How to use Hub Space

There are three primary ways to upload your files:

  1. Upload an individual set of binary-indexed files for immediate visualization. If you have multiple files to upload, Hub Space allows batch uploads by selecting all files at once from your computer.
  2. Upload an entire track hub along with all supporting files (hub.txt, bigWig, bigBed, etc.) to visualize the hub.
  3. To update an existing track hub on Hub Space, you will have to enter the hub's name again. Otherwise, Hub Space assumes that you are trying to create a new hub.

If a hub.txt file is not provided when uploading the data files, a hub.txt file is automatically generated. The generated hub.txt file is configured with the useOneFile trackDb setting, and as a result, each hub is limited to a single genome assembly.

Editing the generated hub.txt file is not yet supported. To customize the hub configuration or data display, replace the generated hub.txt file with your own version after uploading the data files.

By default, your most recently used genome assembly is selected after choosing which files to upload. Use the popular assemblies drop-down menu or the search box to select another genome assembly.

Example of the upload dialog box for Hub Space
Select files for more options
selected.
For information on making track hubs, see the following pages:
You may also contact us if you have any issues or questions on hub development.