Topic
Bigwig
About: Bigwig is a research topic. Over the lifetime, 14 publications have been published within this topic receiving 1614 citations.
Papers
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TL;DR: BigWig and BigBed files are compressed binary indexed files containing data at several resolutions that allow the high-performance display of next-generation sequencing experiment results in the UCSC Genome Browser, enabling fast remote access to large distributed data sets.
Abstract: Summary: BigWig and BigBed files are compressed binary indexed files containing data at several resolutions that allow the high-performance display of next-generation sequencing experiment results in the UCSC Genome Browser. The visualization is implemented using a multi-layered software approach that takes advantage of specific capabilities of web-based protocols and Linux and UNIX operating systems files, R trees and various indexing and compression tricks. As a result, only the data needed to support the current browser view is transmitted rather than the entire file, enabling fast remote access to large distributed data sets.
Availability and implementation: Binaries for the BigWig and BigBed creation and parsing utilities may be downloaded at http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/. Source code for the creation and visualization software is freely available for non-commercial use at http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, implemented in C and supported on Linux. The UCSC Genome Browser is available at http://genome.ucsc.edu
Contact: [email protected]
Supplementary information: Supplementary byte-level details of the BigWig and BigBed file formats are available at Bioinformatics online. For an in-depth description of UCSC data file formats and custom tracks, see http://genome.ucsc.edu/FAQ/FAQformat.html and http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html
1,243 citations
TL;DR: CrossMap is a versatile and efficient tool for converting genome coordinates between assemblies, which supports most of the commonly used file formats, including BAM, sequence alignment map, Wiggle, BigWig, browser extensible data, general feature format, gene transfer format and variant call format.
Abstract: Motivation: Reference genome assemblies are subject to change and refinement from time to time. Generally, researchers need to convert the results that have been analyzed according to old assemblies to newer versions, or vice versa, to facilitate meta-analysis, direct comparison, data integration and visualization. Several useful conversion tools can convert genome interval files in browser extensible data or general feature format, but none have the functionality to convert files in sequence alignment map or BigWig format. This is a significant gap in computational genomics tools, as these formats are the ones most widely used for representing high-throughput sequencing data, such as RNA-seq, chromatin immunoprecipitation sequencing, DNA-seq, etc.
Results: Here we developed CrossMap, a versatile and efficient tool for converting genome coordinates between assemblies. CrossMap supports most of the commonly used file formats, including BAM, sequence alignment map, Wiggle, BigWig, browser extensible data, general feature format, gene transfer format and variant call format.
Availability and implementation: CrossMap is written in Python and C. Source code and a comprehensive user’s manual are freely available at: http://crossmap.sourceforge.net/.
Contact: ude.oyam@erreiPnaeJ.rehcoK or ude.oyam@ougil.gnaw
Supplementary information: Supplementary data are available at Bioinformatics online.
721 citations
TL;DR: Bwtool is a tool designed to read bigWig files rapidly and efficiently, providing functionality for extracting data and summarizing it in several ways, globally or at specific regions, as well as enabling the conversion of the positions of signal data from one genome assembly to another.
Abstract: BigWig files are a compressed, indexed, binary format for genomewide signal data for calculations (e.g. GC percent) or experiments (e.g. ChIP-seq/RNA-seq read depth). bwtool is a tool designed to read bigWig files rapidly and efficiently, providing functionality for extracting data and summarizing it in several ways, globally or at specific regions. Additionally, the tool enables the conversion of the positions of signal data from one genome assembly to another, also known as ‘lifting’. We believe bwtool can be useful for the analyst frequently working with bigWig data, which is becoming a standard format to represent functional signals along genomes. The article includes supplementary examples of running the software. Availability and implementation: TheCsourcecodeisfreelyavailable under the GNU public license v3 at http://cromatina.crg.eu/bwtool. Contact: andrew.pohl@crg.eu, andypohl@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.
257 citations
1 Jun 2001
TL;DR: A static analysis ofwig programs that efficiently decides if all dynamically computed XHTML documents presented to the client will validate according to the official DTD is described.
Abstract: We describe a static analysis of \bigwig\ programs that efficiently decides if all dynamically computed XHTML documents presented to the client will validate according to the official DTD. We employ two data-flow analyses to construct a graph summarizing the possible documents. This graph is subsequently analyzed to determine validity of those documents. By evaluating the technique on a number of realistic benchmarks, we demonstrate that it is sufficiently fast and precise to be practically useful.
67 citations
TL;DR: Steele et al. as mentioned in this paper present a syntax macro language that allows the arguments of a macro to be inductively defined in a meta level grammar and morphed into the host language.
Abstract: "From now on, a main goal in designing a language should be to plan for growth." Guy Steele: Growing a Language, OOPSLA '98 invited talk.We present our experiences with a syntax macro language which we claim forms a general abstraction mechanism for growing (domain-specific) extensions of programming languages. Our syntax macro language is designed to guarantee type safety and termination.A concept of metamorphisms allows the arguments of a macro to be inductively defined in a meta level grammar and morphed into the host language. We also show how the metamorphisms can be made to operate simultaneously on multiple parse trees at once. The result is a highly flexible mechanism for growing new language constructs without resorting to compile-time programming. In fact, whole new languages can be defined at surprisingly low cost.This work is fully implemented as part of the bigwig system for defining interactive Web services, but could find use in many other languages.
21 citations
Related Topics (5)
Performance Metrics
| Year | Papers |
|---|---|
| 2020 | 2 |
| 2017 | 1 |
| 2014 | 6 |
| 2010 | 1 |
| 2008 | 1 |
| 2003 | 1 |