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.

Assembly:
Display Hub Name Description AssembliesClick to connect and browse directly
454 K562andHelaS3RNAseq ERROR: Couldn't open http://web.stanford.edu/~htilgner/2012_454paper/data/hub.txt Debug Help hg19
Blueprint Hub Blueprint Epigenomics Data Hub hg38
BrainEpigenomeHub DNA methylation, chromatin accessibility, and gene expression data from NeuN flow-sorted human brain samples hg19
Breast Cancer lncRNA Breast Cancer lncRNA PMID 26236012 hg19
Broad Improved Canine Annotation v1 Broad Institute CanFam3 Improved Annotation Data v1 canFam3
C_elegans_isolates C. elegans wild isolate assembly hub [+] CB4856Princeton_JR-contig...
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
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 ERROR: Couldn't open https://biochem.wisc.edu/sites/default/files/labs/pike/genome-ucsc/GSE79815_MSC_HUB/hub.txt Debug Help mm9
ChromosomeAssembliesGR ERROR: TCP non-blocking connect() to sftp.rvc.ac.uk IP 195.195.217.212 timed-out in select() after 10000 milliseconds - Cancelling! Couldn't open http://sftp.rvc.ac.uk/rvcpaper/birdsHUB/hub.txt Debug Help colLiv2, galGal4, falPer2
Cotney Lab Human Craniofacial Epigenomics Human Embryonic Craniofacial Tissue Epigenomic Data and Chromatin State Segmentations from the Cotney Lab at UConn Health hg19, mm9
CPTAC Hub v1 ERROR: Host openslice.fenyolab.org not found --> Name or service not known Couldn't open http://openslice.fenyolab.org/tracks/CPTAC/cptac/v1/hub.txt Debug Help hg19
Croc and Bird Hub Croc, Bird, and Archosaur Assembly Hub [+] allMis2, Anc00, Anc01, Anc02, Anc03, Anc04, Anc06...
dan_rer ZGA Hub ERROR: Couldn't open https://slapp04.mssm.edu/auxil/myHub/hub.txt Debug Help danRer10
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
DNA Methylation Hundreds of analyzed methylomes from bisulfite sequencing data [+] hg38, hg19, hg18, mm9, mm10, panTro2, panTro4, ponAbe2...
ENCODE Analysis Hub ENCODE Integrative Analysis Data Hub hg19
Ensembl Regulatory Build Evidence summaries and provisional results for the new Ensembl Regulatory Build hg38, hg19, mm10
EPD Viewer Hub ERROR: Couldn't open http://epd.vital-it.ch/ucsc/epdHubCustomSpecies/epdHubCustomSpecies.txt Debug Help [+] hg19, hg38, mm9, danRer7, rheMac8, galGal5, rn6...
FaceBase Hub ERROR: Couldn't open http://trackhub.facebase.org/hub.txt Debug Help mm9, mm10, hg18, hg19
FANTOM5 RIKEN FANTOM5 Phase1 and Phase2 data hg38, mm10, hg19, mm9, canFam3, rn6, rheMac8
FANTOM5 CAGE RECLU DATA RIKEN FANTOM5 CAGE clusters by RECLU hg19, hg18
GeneHancer ERROR: Couldn't open https://genecards.weizmann.ac.il/geneloc/gh_hub/hub.txt Debug Help hg38, hg19
GRC Genome Issues under Review Genome Reference Consortium: Genome issues and other features hg38, hg19, mm10, mm9, danRer7, danRer10, danRer11
GTEx Analysis Hub Allele-Specific Expression in 53 tissues from GTEx Analysis (NY Genome Center) hg19, hg38
GTEx RNA-seq Signal Hub RNA-seq read coverage in 53 tissues from GTEx V6 (7572 samples) hg19, hg38
Hippocampal DNA methylation and gene transcription ERROR: getaddrinfo() error on hostName=public.hpcagrogenomics.wur.nl: Name or service not known Couldn't open http://public.hpcagrogenomics.wur.nl/ABGC/Track_Hubs/Cognition/hub.txt Debug Help susScr3
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 Islet lncRNAs ERROR: Couldn't open http://www.imperial.ac.uk/medicine/beta-cell-genome-regulation-laboratory/data/HILNCs/HILNCs.txt Debug Help hg19
human p53 Binding And Expression Resource (BAER) hub human p53 ChIP-seq coverage depth (tracks) & SISSRs peak calls with associated differential gene expression from published data as of May 2015 hg19
IDEAS roadmap 20states Roadmap Epigenomics 20 state genome segmentation using the IDEAS algorithm hg19
iPSCORE_RPE ERROR: Couldn't open http://flh1.ucsd.edu/RPE_public/iPSCORE_RPE/hub.txt Debug Help hg19
JASPAR 2018 TFBS TFBS predictions for all profiles in the JASPAR CORE collection (2018) hg19, hg38, ce10, dm6, sacCer3, danRer10, mm10
LIBD Human DLPFC Development RNAseq data across human brain development by age group from LIBD hg19
LNCipedia 5.2 ERROR: Couldn't open https://www.lncipedia.org/trackhub/hub.txt Debug Help hg19, hg38
McGill EMC (CEEHRC) ERROR: Couldn't open http://epigenomesportal.ca/hub/hub.txt Debug Help hg19
MGI Alleles and Phenotypes Allele's and Phenotypes from the Mouse Genome Informatics (MGI) consortium mm10
miRcode microRNA sites Predicted microRNA target sites in GENCODE transcripts hg19
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...
Peptide evidences CNIO Peptides detected from a re-analysis of multiple experiments and databases hg38, hg19
Peterhof_yeasts ERROR: Host public.dobzhanskycenter.ru not found --> Name or service not known Couldn't open http://public.dobzhanskycenter.ru/PeterhofYeastHub/hub.txt Debug Help [+] sacCer3, 1B_D1606_spades...
PhyloCSF Evolutionary protein-coding potential as measured by PhyloCSF hg19, hg38, mm10, galGal4, dm6, ce11
Plants CSHL Biology of Genomes meeting 2013 demonstration assembly hub araTha1, braRap1, ricCom1
Porcine DNA methylation ERROR: Host public.hpcagrogenomics.wur.nl not found --> Name or service not known Couldn't open http://public.hpcagrogenomics.wur.nl/ABGC/Track_Hubs/Chankyu/hub.txt Debug Help susScr3
Porcine DNA methylation and gene transcription ERROR: getaddrinfo() error on hostName=public.hpcagrogenomics.wur.nl: Name or service not known Couldn't open http://public.hpcagrogenomics.wur.nl/ABGC/Track_Hubs/TJ_Tabasco/hub.txt Debug Help susScr3
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
ReMap Regulatory Atlas ERROR: TCP non-blocking connect() to pedagogix-tagc.univ-mrs.fr IP 139.124.66.4 timed-out in select() after 10000 milliseconds - Cancelling! Couldn't open http://pedagogix-tagc.univ-mrs.fr/remap/hubDirectory/trackhub/hub.txt Debug Help hg38
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
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
Translation Initiation Sites (TIS) Translation Initiation Sites (TIS) track hg19
UCD Methylation ERROR: TCP non-blocking connect() to lasallelab.genomecenter.ucdavis.edu timed-out in select() after 10000 milliseconds - Cancelling! Couldn't open http://lasallelab.genomecenter.ucdavis.edu/UCSChub/hub.txt Debug Help [+] hg19, hg18, mm10, mm9, bosTau7, bosTau6, canFam3...
Ultraconserved Elements Ultra conserved Elements in the Human Genome. Science 304(5675) pp.1321-1325 (2004) hg19
Umap and Bismap mappability ERROR: Couldn't open https://pmgenomics.ca/hoffmanlab/proj/bismap/trackhub/hub.txt Debug Help hg38, hg19, mm9, mm10
UMassMed ZHub ERROR: Couldn't open http://zlab-trackhub.umassmed.edu/shulhah/hub.txt Debug Help hg19
UniProt Features ERROR: ftp server response timed out > 1000000 microsec Couldn't open ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/genome_annotation_tracks/UP000005640_9606_hub/hub.txt Debug Help hg38
Vista Enhancers Vista Browser Track Hub hg19, mm9, mm10
WormBase ERROR: Host hubs.yllb.de not found --> Name or service not known Couldn't open http://hubs.yllb.de/pub/databases/wormbase/releases/current-production-release/MULTI_SPECIES/hub/hub.txt Debug Help [+] brenneri, japonica, remanei, ovolvulus, briggsae...
ZebrafishGenomics Burgess Lab Zebrafish Genomic Resources danRer10, danRer7
454 K562andHelaS3RNAseq ERROR: Couldn't open http://web.stanford.edu/~htilgner/2012_454paper/data/hub.txt Debug Help hg19
Blueprint Hub Blueprint Epigenomics Data Hub hg38
BrainEpigenomeHub DNA methylation, chromatin accessibility, and gene expression data from NeuN flow-sorted human brain samples hg19
Breast Cancer lncRNA Breast Cancer lncRNA PMID 26236012 hg19
Broad Improved Canine Annotation v1 Broad Institute CanFam3 Improved Annotation Data v1 canFam3
C_elegans_isolates C. elegans wild isolate assembly hub [+] CB4856Princeton_JR-contig...
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
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 ERROR: Couldn't open https://biochem.wisc.edu/sites/default/files/labs/pike/genome-ucsc/GSE79815_MSC_HUB/hub.txt Debug Help mm9
ChromosomeAssembliesGR ERROR: TCP non-blocking connect() to sftp.rvc.ac.uk IP 195.195.217.212 timed-out in select() after 10000 milliseconds - Cancelling! Couldn't open http://sftp.rvc.ac.uk/rvcpaper/birdsHUB/hub.txt Debug Help colLiv2, galGal4, falPer2
Cotney Lab Human Craniofacial Epigenomics Human Embryonic Craniofacial Tissue Epigenomic Data and Chromatin State Segmentations from the Cotney Lab at UConn Health hg19, mm9
CPTAC Hub v1 ERROR: Host openslice.fenyolab.org not found --> Name or service not known Couldn't open http://openslice.fenyolab.org/tracks/CPTAC/cptac/v1/hub.txt Debug Help hg19
Croc and Bird Hub Croc, Bird, and Archosaur Assembly Hub [+] allMis2, Anc00, Anc01, Anc02, Anc03, Anc04, Anc06...
dan_rer ZGA Hub ERROR: Couldn't open https://slapp04.mssm.edu/auxil/myHub/hub.txt Debug Help danRer10
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
DNA Methylation Hundreds of analyzed methylomes from bisulfite sequencing data [+] hg38, hg19, hg18, mm9, mm10, panTro2, panTro4, ponAbe2...
ENCODE Analysis Hub ENCODE Integrative Analysis Data Hub hg19
Ensembl Regulatory Build Evidence summaries and provisional results for the new Ensembl Regulatory Build hg38, hg19, mm10
EPD Viewer Hub ERROR: Couldn't open http://epd.vital-it.ch/ucsc/epdHubCustomSpecies/epdHubCustomSpecies.txt Debug Help [+] hg19, hg38, mm9, danRer7, rheMac8, galGal5, rn6...
FaceBase Hub ERROR: Couldn't open http://trackhub.facebase.org/hub.txt Debug Help mm9, mm10, hg18, hg19
FANTOM5 RIKEN FANTOM5 Phase1 and Phase2 data hg38, mm10, hg19, mm9, canFam3, rn6, rheMac8
FANTOM5 CAGE RECLU DATA RIKEN FANTOM5 CAGE clusters by RECLU hg19, hg18
GeneHancer ERROR: Couldn't open https://genecards.weizmann.ac.il/geneloc/gh_hub/hub.txt Debug Help hg38, hg19
GRC Genome Issues under Review Genome Reference Consortium: Genome issues and other features hg38, hg19, mm10, mm9, danRer7, danRer10, danRer11
GTEx Analysis Hub Allele-Specific Expression in 53 tissues from GTEx Analysis (NY Genome Center) hg19, hg38
GTEx RNA-seq Signal Hub RNA-seq read coverage in 53 tissues from GTEx V6 (7572 samples) hg19, hg38
Hippocampal DNA methylation and gene transcription ERROR: getaddrinfo() error on hostName=public.hpcagrogenomics.wur.nl: Name or service not known Couldn't open http://public.hpcagrogenomics.wur.nl/ABGC/Track_Hubs/Cognition/hub.txt Debug Help susScr3
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 Islet lncRNAs ERROR: Couldn't open http://www.imperial.ac.uk/medicine/beta-cell-genome-regulation-laboratory/data/HILNCs/HILNCs.txt Debug Help hg19
human p53 Binding And Expression Resource (BAER) hub human p53 ChIP-seq coverage depth (tracks) & SISSRs peak calls with associated differential gene expression from published data as of May 2015 hg19
IDEAS roadmap 20states Roadmap Epigenomics 20 state genome segmentation using the IDEAS algorithm hg19
iPSCORE_RPE ERROR: Couldn't open http://flh1.ucsd.edu/RPE_public/iPSCORE_RPE/hub.txt Debug Help hg19
JASPAR 2018 TFBS TFBS predictions for all profiles in the JASPAR CORE collection (2018) hg19, hg38, ce10, dm6, sacCer3, danRer10, mm10
LIBD Human DLPFC Development RNAseq data across human brain development by age group from LIBD hg19
LNCipedia 5.2 ERROR: Couldn't open https://www.lncipedia.org/trackhub/hub.txt Debug Help hg19, hg38
McGill EMC (CEEHRC) ERROR: Couldn't open http://epigenomesportal.ca/hub/hub.txt Debug Help hg19
MGI Alleles and Phenotypes Allele's and Phenotypes from the Mouse Genome Informatics (MGI) consortium mm10
miRcode microRNA sites Predicted microRNA target sites in GENCODE transcripts hg19
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...
Peptide evidences CNIO Peptides detected from a re-analysis of multiple experiments and databases hg38, hg19
Peterhof_yeasts ERROR: Host public.dobzhanskycenter.ru not found --> Name or service not known Couldn't open http://public.dobzhanskycenter.ru/PeterhofYeastHub/hub.txt Debug Help [+] sacCer3, 1B_D1606_spades...
PhyloCSF Evolutionary protein-coding potential as measured by PhyloCSF hg19, hg38, mm10, galGal4, dm6, ce11
Plants CSHL Biology of Genomes meeting 2013 demonstration assembly hub araTha1, braRap1, ricCom1
Porcine DNA methylation ERROR: Host public.hpcagrogenomics.wur.nl not found --> Name or service not known Couldn't open http://public.hpcagrogenomics.wur.nl/ABGC/Track_Hubs/Chankyu/hub.txt Debug Help susScr3
Porcine DNA methylation and gene transcription ERROR: getaddrinfo() error on hostName=public.hpcagrogenomics.wur.nl: Name or service not known Couldn't open http://public.hpcagrogenomics.wur.nl/ABGC/Track_Hubs/TJ_Tabasco/hub.txt Debug Help susScr3
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
ReMap Regulatory Atlas ERROR: TCP non-blocking connect() to pedagogix-tagc.univ-mrs.fr IP 139.124.66.4 timed-out in select() after 10000 milliseconds - Cancelling! Couldn't open http://pedagogix-tagc.univ-mrs.fr/remap/hubDirectory/trackhub/hub.txt Debug Help hg38
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
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
Translation Initiation Sites (TIS) Translation Initiation Sites (TIS) track hg19
UCD Methylation ERROR: TCP non-blocking connect() to lasallelab.genomecenter.ucdavis.edu timed-out in select() after 10000 milliseconds - Cancelling! Couldn't open http://lasallelab.genomecenter.ucdavis.edu/UCSChub/hub.txt Debug Help [+] hg19, hg18, mm10, mm9, bosTau7, bosTau6, canFam3...
Ultraconserved Elements Ultra conserved Elements in the Human Genome. Science 304(5675) pp.1321-1325 (2004) hg19
Umap and Bismap mappability ERROR: Couldn't open https://pmgenomics.ca/hoffmanlab/proj/bismap/trackhub/hub.txt Debug Help hg38, hg19, mm9, mm10
UMassMed ZHub ERROR: Couldn't open http://zlab-trackhub.umassmed.edu/shulhah/hub.txt Debug Help hg19
UniProt Features ERROR: ftp server response timed out > 1000000 microsec Couldn't open ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/genome_annotation_tracks/UP000005640_9606_hub/hub.txt Debug Help hg38
Vista Enhancers Vista Browser Track Hub hg19, mm9, mm10
WormBase ERROR: Host hubs.yllb.de not found --> Name or service not known Couldn't open http://hubs.yllb.de/pub/databases/wormbase/releases/current-production-release/MULTI_SPECIES/hub/hub.txt Debug Help [+] brenneri, japonica, remanei, ovolvulus, briggsae...
ZebrafishGenomics Burgess Lab Zebrafish Genomic Resources 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. 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.

Contact us if you wish to submit a hub to the list of public hubs.

Display Hub Name Description AssembliesClick to connect and browse directly
Plant araTha1 Plant araTha1 Hub araTha1

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.