WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis

被引：113

作者：

Zerbino, Daniel R. ^{[1
]}

Johnson, Nathan ^{[1
]}

Juettemann, Thomas ^{[1
]}

Wilder, Steven P. ^{[1
]}

Flicek, Paul ^{[1
]}

机构：

[1] European Bioinformat Inst EMBL EBI, European Mol Biol Lab, Cambridge CB10 1SD, England

来源：

BIOINFORMATICS | 2014年 / 30卷 / 07期

基金：

英国惠康基金;

关键词：

D O I：

10.1093/bioinformatics/btt737

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Motivation: Using high-throughput sequencing, researchers are now generating hundreds of whole-genome assays to measure various features such as transcription factor binding, histone marks, DNA methylation or RNA transcription. Displaying so much data generally leads to a confusing accumulation of plots. We describe here a multithreaded library that computes statistics on large numbers of datasets (Wiggle, BigWig, Bed, BigBed and BAM), generating statistical summaries within minutes with limited memory requirements, whether on the whole genome or on selected regions.

引用

页码：1008 / 1009

页数：2

共 9 条

[1] BLUEPRINT to decode the epigenetic signature written in blood [J].

Adams, David ;

Altucci, Lucia ;

Antonarakis, Stylianos E. ;

Ballesteros, Juan ;

Beck, Stephan ;

Bird, Adrian ;

Bock, Christoph ;

Boehm, Bernhard ;

Campo, Elias ;

Caricasole, Andrea ;

Dahl, Fredrik ;

Dermitzakis, Emmanouil T. ;

Enver, Tariq ;

Esteller, Manel ;

Estivill, Xavier ;

Ferguson-Smith, Anne ;

Fitzgibbon, Jude ;

Flicek, Paul ;

Giehl, Claudia ;

Graf, Thomas ;

Grosveld, Frank ;

Guigo, Roderic ;

Gut, Ivo ;

Helin, Kristian ;

Jarvius, Jonas ;

Kueppers, Ralf ;

Lehrach, Hans ;

Lengauer, Thomas ;

Lernmark, Ake ;

Leslie, David ;

Loeffler, Markus ;

Macintyre, Elizabeth ;

Mai, Antonello ;

Martens, Joost H. A. ;

Minucci, Saverio ;

Ouwehand, Willem H. ;

Pelicci, Pier Giuseppe ;

Pendeville, Helene ;

Porse, Bo ;

Rakyan, Vardhman ;

Reik, Wolf ;

Schrappe, Martin ;

Schuebeler, Dirk ;

Seifert, Martin ;

Siebert, Reiner ;

Simmons, David ;

Soranzo, Nicole ;

Spicuglia, Salvatore ;

Stratton, Michael ;

Stunnenberg, Hendrik G. .

NATURE BIOTECHNOLOGY, 2012, 30 (03) :224-226

[2]

[Anonymous], 2019, R: A language for environment for statistical computing

[3]

Barroso I, 2012, NATURE, V489, P54

[4] The NIH Roadmap Epigenomics Mapping Consortium [J].

Bernstein, Bradley E. ;

Stamatoyannopoulos, John A. ;

Costello, Joseph F. ;

Ren, Bing ;

Milosavljevic, Aleksandar ;

Meissner, Alexander ;

Kellis, Manolis ;

Marra, Marco A. ;

Beaudet, Arthur L. ;

Ecker, Joseph R. ;

Farnham, Peggy J. ;

Hirst, Martin ;

Lander, Eric S. ;

Mikkelsen, Tarjei S. ;

Thomson, James A. .

NATURE BIOTECHNOLOGY, 2010, 28 (10) :1045-1048

[5] Ensembl 2013 [J].

Flicek, Paul ;

Ahmed, Ikhlak ;

Amode, M. Ridwan ;

Barrell, Daniel ;

Beal, Kathryn ;

Brent, Simon ;

Carvalho-Silva, Denise ;

Clapham, Peter ;

Coates, Guy ;

Fairley, Susan ;

Fitzgerald, Stephen ;

Gil, Laurent ;

Garcia-Giron, Carlos ;

Gordon, Leo ;

Hourlier, Thibaut ;

Hunt, Sarah ;

Juettemann, Thomas ;

Kaehaeri, Andreas K. ;

Keenan, Stephen ;

Komorowska, Monika ;

Kulesha, Eugene ;

Longden, Ian ;

Maurel, Thomas ;

McLaren, William M. ;

Muffato, Matthieu ;

Nag, Rishi ;

Overduin, Bert ;

Pignatelli, Miguel ;

Pritchard, Bethan ;

Pritchard, Emily ;

Riat, Harpreet Singh ;

Ritchie, Graham R. S. ;

Ruffier, Magali ;

Schuster, Michael ;

Sheppard, Daniel ;

Sobral, Daniel ;

Taylor, Kieron ;

Thormann, Anja ;

Trevanion, Stephen ;

White, Simon ;

Wilder, Steven P. ;

Aken, Bronwen L. ;

Birney, Ewan ;

Cunningham, Fiona ;

Dunham, Ian ;

Harrow, Jennifer ;

Herrero, Javier ;

Hubbard, Tim J. P. ;

Johnson, Nathan ;

Kinsella, Rhoda .

NUCLEIC ACIDS RESEARCH, 2013, 41 (D1) :D48-D55

[6] BigWig and BigBed: enabling browsing of large distributed datasets [J].

Kent, W. J. ;

Zweig, A. S. ;

Barber, G. ;

Hinrichs, A. S. ;

Karolchik, D. .

BIOINFORMATICS, 2010, 26 (17) :2204-2207

[7] The Sequence Alignment/Map format and SAMtools [J].

Li, Heng ;

Handsaker, Bob ;

Wysoker, Alec ;

Fennell, Tim ;

Ruan, Jue ;

Homer, Nils ;

Marth, Gabor ;

Abecasis, Goncalo ;

Durbin, Richard .

BIOINFORMATICS, 2009, 25 (16) :2078-2079

[8] The UCSC Genome Browser database: extensions and updates 2013 [J].

Meyer, Laurence R. ;

Zweig, Ann S. ;

Hinrichs, Angie S. ;

Karolchik, Donna ;

Kuhn, Robert M. ;

Wong, Matthew ;

Sloan, Cricket A. ;

Rosenbloom, Kate R. ;

Roe, Greg ;

Rhead, Brooke ;

Raney, Brian J. ;

Pohl, Andy ;

Malladi, Venkat S. ;

Li, Chin H. ;

Lee, Brian T. ;

Learned, Katrina ;

Kirkup, Vanessa ;

Hsu, Fan ;

Heitner, Steve ;

Harte, Rachel A. ;

Haeussler, Maximilian ;

Guruvadoo, Luvina ;

Goldman, Mary ;

Giardine, Belinda M. ;

Fujita, Pauline A. ;

Dreszer, Timothy R. ;

Diekhans, Mark ;

Cline, Melissa S. ;

Clawson, Hiram ;

Barber, Galt P. ;

Haussler, David ;

Kent, W. James .

NUCLEIC ACIDS RESEARCH, 2013, 41 (D1) :D64-D69

[9] BEDTools: a flexible suite of utilities for comparing genomic features [J].

Quinlan, Aaron R. ;

Hall, Ira M. .

BIOINFORMATICS, 2010, 26 (06) :841-842

← 1 →