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

Brian J. Raney; 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

doi:10.1093/bioinformatics/btt637

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

Brian J. Raney, 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

Research output: Contribution to journal › Article › peer-review

282 Scopus citations

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.Contact:

Original language	English
Pages (from-to)	1003-1005
Number of pages	3
Journal	Bioinformatics
Volume	30
Issue number	7
DOIs	https://doi.org/10.1093/bioinformatics/btt637
State	Published - Apr 1 2014

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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.Contact:",

author = "Raney, {Brian J.} and Dreszer, {Timothy R.} and Barber, {Galt P.} and Hiram Clawson and Fujita, {Pauline A.} and Ting Wang and Ngan Nguyen and Benedict Paten and Zweig, {Ann S.} and Donna Karolchik and Kent, {W. James}",

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AU - Fujita, Pauline A.

AU - Wang, Ting

AU - Nguyen, Ngan

AU - Paten, Benedict

AU - Zweig, Ann S.

AU - Karolchik, Donna

AU - Kent, W. James

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N2 - 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.Contact:

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

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