Thank you Kate Rosenbloom and Daniel Schmelter for developing and releasing these tracks
++We have released a new video to the Browser's +YouTube channel. +
+ ++ Browser Basics, Part Three — Configuring the Browser + + DNA navigation +
+ ++This video +is part of a three-part series that goes back to the Basics, +designed to introduce new users to the Browser. + +Our previous videos have been directed +either at experienced users who may have questions about how to do certain +tasks, or serve as introductions to new features in the Browser. +In this three-part series, we fill in the background with more basic +information, though we expect experienced users to find some new things +as well. +
+ ++Today's release, Part Three, shows further configuration options +in the Browser and also how to use DNA sequence to find locations +in the genome. Examples include BLAT, Short Match, Drag-N-Highlight, +removing highlights, Drag-N-Zoom, configuring the scale bar/base position +track, adding a title to the image and more. +
+ ++As is our practice, a transcript +is provided for those who wish to review the content before watching. +
+ ++Thanks to Robert Kuhn for the video production. +
+ +We are pleased to announce new NCBI RefSeq assembly hubs for vertebrate genomes. Currently these hubs contain 295 assemblies, encompassing most RefSeq vertebrate genomes.
All assemblies contain multiple gene models including NCBI RefSeq annotations, and Ensembl gene predictions where available. Additional tracks include repeat masking and simple repeat data. A complete list of available tracks for each assembly can be found in the respective track statistics page.
The assemblies are divided into 5 categories, see the assembly statistics link below for a complete list of available genomes in each hub. Assembly statistics such as genome size, gaps, and masking are also available for each genome. Lastly, track statistics are also available displaying all available tracks for each assembly, as well as their genomic coverage.
Details on each release can be found on the GENCODE site. This includes statistics on each release.
We would like to thank the GENCODE project for providing these annotations. We would also like to thank Mark Diekhans and Daniel Schmelter for the development and release of these tracks.
+We are excited to announce an update to the GTEx V8 for the gene expression track
based on data from the
NIH Genotype-Tissue Expression (GTEx) project. This track displays
tissue-specific gene expression based on RNA-seq in 54 tissues from 948 donors
released in August 2019.
The original data for this track can be found at the GTEX Portalhosted by the Broad Institute.
This track features a horizontal bar chart for each GENCODE gene, resulting in
colored bars which show median tissue expression values assayed by the GTEx project in RPKM.
Mouse over the bar in the graph shows a tissue specific expression value, while clicking on a chart
shows a much larger box-and-wiskers graph for that transcript. The complete tissue color legend
and filters are shown on the
Thank you Kate Rosenbloom and Daniel Schmelter for developing and releasing these tracks
We are pleased to announce the release of a new video on our YouTube channel, designed to help make the Browser more accessible to those not usually using the Genome Browser, especially virologists and molecular biologists developing assays and vaccines. The video highlights many features that regular Browser users may already know, but in the context of SARS-CoV-2 genome assembly. The Browser coronavirus tour highlights RT-PCR data, UniProt , crowd-sourced data, T-cell Reactive epitopes and comparative genomics data for viral isolates from around the world and those @@ -469,82 +530,83 @@
We are pleased to announce two new Genome Aggregation Database (gnomAD) tracks, Predicted Constraint Metrics and Structural Variants, for the human (GRCh37/hg19) assembly.
-This data shows various metrics of pathogenicity per-gene as predicted for gnomAD v2.1.1 and +These data show various metrics of pathogenicity per-gene as predicted for gnomAD v2.1.1 and identifies genes subject to strong selection against various classes of mutation. It is comprised of three subtracks:
-This data shows structural variants calls (>=50 nucleotides) from the gnomAD v2.1 release on +These data show structural variants calls (>=50 nucleotides) from the gnomAD v2.1 release on 10,847 unrelated genomes. It is comprised of three subtracks:
-This data can be found as part of the gnomAD super-track. More information on this track can be found in the track description pages, as well as the gnomAD site.
We would like to thank the Genome Aggregation Database Consortium for making these data available. We would also like to thank Christopher Lee, Maximilian Haeussler, Lou Nassar, Jairo Navarro, Robert Kuhn and Anna Benet-Pages for their effort in the creation of these tracks.
+Apr. 20, 2020 New video on the Browser's YouTube channelWe have released a new video to the Browser's YouTube channel.
Browser Basics, Part Two — Configuring the Browser
This video @@ -783,41 +845,41 @@
In summary, this track provides a functional canonical gene set until the MANE set is complete. More information on this track and data can be found in the track description page, NCBI's RefSeq Select page, and the MANE page.
We would like to thank NCBI for releasing the RefSeq Select data, as well as the NCBI and -Ensembl-GENCODE collaboration for MANE. We would also like to thank Max Haeussler and Lou +Ensembl-GENCODE collaboration for MANE. We would also like to thank Max Haussler and Lou Nassar for the development and release of these tracks.
We are pleased to announce new GENCODE Gene annotation tracks, which correspond to Ensembl 99, for three assemblies: hg19/GRCh37, hg38/GRCh38, and mm10/GRCm38. For human, the GENCODE V33 annotations were mapped to hg38/GRCh38 and then back-mapped to the hg19/GRCh37 assembly. For all three assemblies, the gene sets contain the following tracks:
@@ -958,31 +1020,31 @@We are happy to release the updated NCBI RefSeq Annotation Release 109.20190905 track on the Genome Browser. The NCBI RefSeq Genes composite track shows human protein-coding and non-protein-coding genes taken from the NCBI RNA reference sequences collection (RefSeq). This update adds more than 500 new gene entries to the collection of nearly 167,000 annotations. More information can be found on the track description pages for these composite tracks for hg19 and hg38.
We would like to thank NCBI and the RefSeq Annotation database for collecting and curating -this data. We would also like to thank Hiram Clawson and Daniel Schmelter for their role +these data. We would also like to thank Hiram Clawson and Daniel Schmelter for their role creating, documenting, and reviewing these tracks.
We are pleased to announce a new track, Avada Variants, now available on hg19. Additionally, we have updated the Mastermind Variants track and expanded it to hg38.
We are pleased to announce a new dbSNP pipeline, along with the first new dataset: dbSNP b153 for hg19 and hg38.
dbSNP has seen an explosive growth in recent releases, from roughly 324 million variants in build 150, to over 700 million variants in the latest build b153. In an effort to continue -providing efficient access to this data, dbSNP has redesigned their architecture and data flow. We have also taken this opportunity to redesign our dbSNP ingestion pipeline. Below is a short summary of the UCSC changes brought forth by both dbSNP's redesign, as well as UCSC's new pipeline.
"SNPs" tracks were previously based on related mysql database tables, but the new bigDbSnp format is a bigBed file with extra columns that contains all necessary information @@ -1115,62 +1177,62 @@
While processing the information downloaded from dbSNP, UCSC annotates some properties of interest. These are noted on the item details page, and may be used to include or exclude affected variants. These UCSC notes (currently 26) can be divided into three categories:
-With the bigDbSnp format, this data will no longer be available as a database table dump. The +With the bigDbSnp format, these data will no longer be available as a database table dump. The complete data can be found across two separate files in our download server, a bigBed file (bigDbSnp) for hg19 and hg38, and a shared secondary details file which holds additional variant details.
Additional information including visibility display, a complete list of UCSC notes, and a methods section can be found in the track description page.
We would like to thanks the dbSNP group at NCBI for providing access to these data. We would also like to thank Angie Hinrichs and the UCSC Genome Browser team for their efforts on this release.
We are pleased to announce the release of the new EPDnew Promoters track for human (hg38 and hg19) and mouse (mm10) assemblies. These tracks represent the experimentally validated promoters generated by the Eukaryotic Promoter Database, based on gene transcript models obtained from multiple sources (HGNC, GENCODE, Ensembl, RefSeq), then validated using data from CAGE and RAMPAGE experimental studies obtained from FANTOM 5, UCSC, and ENCODE. Peak calling, clustering and filtering based on relative expression were applied to identify the most expressed promoters and those present in the largest number of samples.
We would like to thanks Philipp Bucher and the EPD team at the Swiss Bioinformatics Institute for -providing this data, and Kate Rosenbloom and Jairo Navarro at UCSC for creating and reviewing these +providing these data, and Kate Rosenbloom and Jairo Navarro at UCSC for creating and reviewing these tracks.
We are pleased to announce a new Enhancer-Gene Map for the mouse mm10 assembly. This track set presents enhancer-promoter interactions predicted from correlation of enhancer-associated chromatin signals and gene expression across tissue stages, based on histone modification (ChIP-seq) and transcription (RNA-seq) assays and analysis performed in the ENCODE project as part of the Mouse Developmental Series (part of ENCODE phase 3). Data underlying this track are presented in the Histone Modifications and Chromatin State tracks, part of the ENCODE Regulation supertrack. The promoters in this track were derived from experimentally validated promoters provided by the Eukaryotic Promoter Database (EPDNew). A more complete presentation of this annotation can be found in the @@ -1257,31 +1319,31 @@ presents the results of a comprehensive study of chromatin state across these developmental stages, based on 1,128 ChiP-seq assays of 8 histone modifications in 12 tissues.
Thanks to David Gorkin and Yanxiao Zhang at the Ren lab (UCSD/Ludwig Institute for Cancer Research) and Iros Barozzi of the Environmental Genomics and Systems Biology Division -at the Lawrence Berkeley National Laboratory for providing this data and assisting with track +at the Lawrence Berkeley National Laboratory for providing these data and assisting with track development at UCSC. We would also like to thank Kate Rosenbloom, Conner Powell and the UCSC Genome Browser team for their efforts on this release.
We are pleased to announce an update to the Locus Reference Genomic (LRG) regions track for human, (GRCh37/hg19) and (GRCh38/hg38). Each LRG record also includes at least one stable transcript on which variants may be reported. These transcripts appear in the LRG Transcripts track in the Gene and Gene Predictions track section.
This track was produced at UCSC using LRG XML files. Thanks to @@ -1350,31 +1412,31 @@ used in GeneHancer, which was made for low-density interactions.
We are pleased to announce the new Platinum Genomes VCF Tracks. These variant tracks -offer deeply sequenced and validated VCFs on both hg19 and hg38. This data was derived from +offer deeply sequenced and validated VCFs on both hg19 and hg38. These data were derived from consensus analysis of a 17-member family pedigree to reduce potential error. You can view the tracks below:
We are pleased to announce the release of updated GENCODE Genes annotation tracks for both the hg38/GRCh38 and mm10/GRCm38 assemblies @@ -1444,31 +1506,31 @@ hg38/GRCh38 assembly. This track shows the DNA sequences targetable by CRISPR RNA guides using the Cas9 enzyme from S. pyogenes (PAM: NGG) over the entire human genome. CRISPR target sites were annotated with predicted specificity (off-target effects) and predicted efficiency (on-target cleavage) by various algorithms through the tool CRISPOR. The target sequence of the guide is shown with a thick (exon) bar. The PAM motif match (NGG) is shown with a thinner bar.
We would like to thank Maximilian Haeussler, Hiram Clawson, and Conner Powell for their effort creating and releasing this data track.
- +We are pleased to announce the release of a GRC Incident track for both the Chicken (galGal6) and Zebrafish (danRer11) assemblies. These tracks show locations in the Chicken and Zebrafish assemblies where assembly problems have been noted or resolved, as reported by the Genome Reference Consortium (GRC).