Learn to use the advanced features, including the Table Browser and custom tracks, of the UCSC Genome Browser with this free tutorial, sponsored by UCSC Genome Bioinformatics Group. The UCSC Genome Browser provides a way to query and extract the data from many genomes, with extensive annotation for various data types including known genes, predicted genes, SNPs, comparative multi-species analysis and much more. Obtain large lists of genes, SNPs, or any other features of interest, or display your own data, using the tools underlying the UCSC Genome Browser. This tutorial is the second in a series of tutorials on the UCSC Genome Browser and explores many aspects beyond the basic search and analysis functions covered in the introductory tutorial.

You will learn:

  • to perform advanced searches of the UCSC genome databases
  • to export and download large quantities of targeted data
  • to create custom tracks resulting from your advanced searches
  • to create custom annotation tracks of your data to share with others
  • to use the Genome Graphs tool for visualizing GWAS data
TUTORIAL RELATED CONTENT

TUTORIALS

This tutorial is a part of the tutorial group UCSC Tutorials. You might find the other tutorials in the group interesting:

ENCODE Foundations: ENCyclopedia of DNA Elements

UCSC Genome Browser: The Additional Tools: Additional tools at the UCSC Genome Browser

UCSC Archaeal Genome Browser: Provides you with many research and analysis tools that can be used to examine the genomes of more than 50 microbial species from the domain archaea.

ENCODE Data at UCSC: ENCODE Data at UCSC

UCSC Genome Browser: An Introduction: The UCSC Genome Browser Introduction

CATEGORIES

Algorithms and Analysis : This category contains various tools that may help perform analysis of different genomics data types. This may include sequence alignment, large-scale or complex queries, motif finding, or comparative assessments.

Genome Databases (euk) : Genomic databases or repositories primarily aimed at eukaryotic organisms. Some may contain prokaryotic data as well.

BLOG POSTS

Video Tip of the Week: Introduction to the UCSC Genome Browser : This week's tip is quite multi-media. There's a video, as required. But there's a traditional published paper format, too. And there's also the free training slides and exercises from us, sponsored by ...

UCSC replaces UCSC Genes with GENCODE as default gene set: This is a big deal. And now I have to change my training materials. But I think it's worthwhile. The GENCODE set is very extensive and the range of annotated types captures important details. This emai...

Video Tip of the Week: ClinGen, The Clinical Genome Resource: The sequence data tsunami begins to crash into the shore, at the feet of clinicians and patients who want answers and treatment directions. But sometimes the tsunami is washing in debris. As the amount...

Video Tip of the Week: TargetMine, Data Warehouse for Drug Discovery: Browsing around genomic regions, layering on lots of associated data, and beginning to explore new data types I might come across are things that really fire up my brain. For me, visualization is key t...

Video Tip of the Week: Viewing Amino Acid info in the UCSC Genome Browser: We've been doing training on the UCSC Genome Browser for over 10 years now. We've seen it grow from just a few genomes and a few tracks to the enormous trove of information it is today. In fact, one of...

BIOMED CENTRAL

Recent BioMed Central research articles citing this resource

Huang Jie et al., Genome-wide survey and analysis of microsatellites in giant panda ( Ailuropoda melanoleuca ), with a focus on the applications of a novel microsatellite marker system. BMC Genomics (2015) doi:10.1186/s12864-015-1268-z

Castellano Leandro et al., The germline of the malaria mosquito produces abundant miRNAs, endo-siRNAs, piRNAs and 29-nt small RNAs. BMC Genomics (2015) doi:10.1186/s12864-015-1257-2

González García Ramón Juan et al., Are submicroscopic chromosomal inversions predisposing factors for the t(9;22)(q34;q11.2) translocation in chronic myeloid leukemia?. Molecular Cytogenetics (2015) doi:10.1186/s13039-015-0116-9

Dobek A Whitney et al., Long-term follow-up of females with unbalanced X;Y translocations—reproductive and nonreproductive consequences. Molecular Cytogenetics (2015) doi:10.1186/s13039-015-0112-0

Fleming D Joseph et al., STAT3 acts through pre-existing nucleosome-depleted regions bound by FOS during an epigenetic switch linking inflammation to cancer. Epigenetics Chromatin (2015) doi:10.1186/1756-8935-8-7