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FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology
Summary: Next-generation sequencing can provide insight into protein–DNA association events on a genome-wide scale, and is being applied in an increasing number of applications in genomics and meta-genomics research. However, few software applications are available for interpreting these experiments...
Autores principales: | , , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2008
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2638869/ https://www.ncbi.nlm.nih.gov/pubmed/18599518 http://dx.doi.org/10.1093/bioinformatics/btn305 |
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author | Fejes, Anthony P. Robertson, Gordon Bilenky, Mikhail Varhol, Richard Bainbridge, Matthew Jones, Steven J. M. |
author_facet | Fejes, Anthony P. Robertson, Gordon Bilenky, Mikhail Varhol, Richard Bainbridge, Matthew Jones, Steven J. M. |
author_sort | Fejes, Anthony P. |
collection | PubMed |
description | Summary: Next-generation sequencing can provide insight into protein–DNA association events on a genome-wide scale, and is being applied in an increasing number of applications in genomics and meta-genomics research. However, few software applications are available for interpreting these experiments. We present here an efficient application for use with chromatin-immunoprecipitation (ChIP-Seq) experimental data that includes novel functionality for identifying areas of gene enrichment and transcription factor binding site locations, as well as for estimating DNA fragment size distributions in enriched areas. The FindPeaks application can generate UCSC compatible custom ‘WIG’ track files from aligned-read files for short-read sequencing technology. The software application can be executed on any platform capable of running a Java Runtime Environment. Memory requirements are proportional to the number of sequencing reads analyzed; typically 4 GB permits processing of up to 40 million reads. Availability: The FindPeaks 3.1 package and manual, containing algorithm descriptions, usage instructions and examples, are available at http://www.bcgsc.ca/platform/bioinfo/software/findpeaks Source files for FindPeaks 3.1 are available for academic use. Contact: afejes@bcgsc.ca |
format | Text |
id | pubmed-2638869 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2008 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-26388692009-02-25 FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology Fejes, Anthony P. Robertson, Gordon Bilenky, Mikhail Varhol, Richard Bainbridge, Matthew Jones, Steven J. M. Bioinformatics Applications Note Summary: Next-generation sequencing can provide insight into protein–DNA association events on a genome-wide scale, and is being applied in an increasing number of applications in genomics and meta-genomics research. However, few software applications are available for interpreting these experiments. We present here an efficient application for use with chromatin-immunoprecipitation (ChIP-Seq) experimental data that includes novel functionality for identifying areas of gene enrichment and transcription factor binding site locations, as well as for estimating DNA fragment size distributions in enriched areas. The FindPeaks application can generate UCSC compatible custom ‘WIG’ track files from aligned-read files for short-read sequencing technology. The software application can be executed on any platform capable of running a Java Runtime Environment. Memory requirements are proportional to the number of sequencing reads analyzed; typically 4 GB permits processing of up to 40 million reads. Availability: The FindPeaks 3.1 package and manual, containing algorithm descriptions, usage instructions and examples, are available at http://www.bcgsc.ca/platform/bioinfo/software/findpeaks Source files for FindPeaks 3.1 are available for academic use. Contact: afejes@bcgsc.ca Oxford University Press 2008-08-01 2008-07-03 /pmc/articles/PMC2638869/ /pubmed/18599518 http://dx.doi.org/10.1093/bioinformatics/btn305 Text en © 2008 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Applications Note Fejes, Anthony P. Robertson, Gordon Bilenky, Mikhail Varhol, Richard Bainbridge, Matthew Jones, Steven J. M. FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology |
title | FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology |
title_full | FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology |
title_fullStr | FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology |
title_full_unstemmed | FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology |
title_short | FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology |
title_sort | findpeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology |
topic | Applications Note |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2638869/ https://www.ncbi.nlm.nih.gov/pubmed/18599518 http://dx.doi.org/10.1093/bioinformatics/btn305 |
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