Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser

doi:10.1093/bioinformatics/btt637

. 2014 Apr 1;30(7):1003-5.

doi: 10.1093/bioinformatics/btt637. Epub 2013 Nov 13.

Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser

Brian J Raney¹, Timothy R Dreszer, Galt P Barber, Hiram Clawson, Pauline A Fujita, Ting Wang, Ngan Nguyen, Benedict Paten, Ann S Zweig, Donna Karolchik, W James Kent

Affiliations

Affiliation

¹ Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA and Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA.

PMID: 24227676
PMCID: PMC3967101
DOI: 10.1093/bioinformatics/btt637

Free PMC article

Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser

Brian J Raney et al. Bioinformatics. 2014.

Free PMC article

. 2014 Apr 1;30(7):1003-5.

doi: 10.1093/bioinformatics/btt637. Epub 2013 Nov 13.

Authors

Brian J Raney¹, Timothy R Dreszer, Galt P Barber, Hiram Clawson, Pauline A Fujita, Ting Wang, Ngan Nguyen, Benedict Paten, Ann S Zweig, Donna Karolchik, W James Kent

Affiliation

¹ Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA and Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA.

PMID: 24227676
PMCID: PMC3967101
DOI: 10.1093/bioinformatics/btt637

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Abstract

Summary: Track data hubs provide an efficient mechanism for visualizing remotely hosted Internet-accessible collections of genome annotations. Hub datasets can be organized, configured and fully integrated into the University of California Santa Cruz (UCSC) Genome Browser and accessed through the familiar browser interface. For the first time, individuals can use the complete browser feature set to view custom datasets without the overhead of setting up and maintaining a mirror.

Availability and implementation: Source code for the BigWig, BigBed and Genome Browser software is freely available for non-commercial use at http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, implemented in C and supported on Linux. Binaries for the BigWig and BigBed creation and parsing utilities may be downloaded at http://hgdownload.cse.ucsc.edu/admin/exe/. Binary Alignment/Map (BAM) and Variant Call Format (VCF)/tabix utilities are available from http://samtools.sourceforge.net/ and http://vcftools.sourceforge.net/. The UCSC Genome Browser is publicly accessible at http://genome.ucsc.edu.

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References

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1. Dowell RD, et al. The distributed annotation system. BMC Bioinformatics. 2001;2:7. - PMC - PubMed
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1. Karolchik D, et al. The UCSC Table Browser data retrieval tool. Nucleic Acids Res. 2004;32:D493–D496. - PMC - PubMed

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[1] Danacek P, et al. The variant call format and VCF tools. Bioinformatics. 2011;27:2156–2158. - PMC - PubMed

[2] Danacek P, et al. The variant call format and VCF tools. Bioinformatics. 2011;27:2156–2158. - PMC - PubMed

[3] Dowell RD, et al. The distributed annotation system. BMC Bioinformatics. 2001;2:7. - PMC - PubMed

[4] Dowell RD, et al. The distributed annotation system. BMC Bioinformatics. 2001;2:7. - PMC - PubMed

[5] Dreszer TR, et al. The UCSC Genome Browser database: extensions and updates 2011. Nucleic Acids Res. 2012;40:D918–D923. - PMC - PubMed

[6] Dreszer TR, et al. The UCSC Genome Browser database: extensions and updates 2011. Nucleic Acids Res. 2012;40:D918–D923. - PMC - PubMed

[7] Flicek P, et al. Ensembl 2013. Nucleic Acids Res. 2013;41:D48–D55. - PMC - PubMed

[8] Flicek P, et al. Ensembl 2013. Nucleic Acids Res. 2013;41:D48–D55. - PMC - PubMed

[9] Karolchik D, et al. The UCSC Table Browser data retrieval tool. Nucleic Acids Res. 2004;32:D493–D496. - PMC - PubMed

[10] Karolchik D, et al. The UCSC Table Browser data retrieval tool. Nucleic Acids Res. 2004;32:D493–D496. - PMC - PubMed

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Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser

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Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser

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Cited by 141 articles

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