TY - GEN
T1 - A scalable, flexible workflow for MethylCap-seq data analysis
AU - Rodriguez, Benjamin
AU - Tam, Hok Hei
AU - Frankhouser, David
AU - Trimarchi, Michael
AU - Murphy, Mark
AU - Kuo, Chris
AU - Parikh, Deval
AU - Ball, Bryan
AU - Schwind, Sebastian
AU - Curfman, John
AU - Blum, William
AU - Marcucci, Guido
AU - Yan, Pearlly
AU - Bundschuh, Ralf
PY - 2011/12/1
Y1 - 2011/12/1
N2 - Advances in whole genome profiling have revolutionized the cancer research field, but at the same time have raised new bioinformatics challenges. For next generation sequencing (NGS), these include data storage, computational costs, sequence processing and alignment, delineating appropriate statistical measures, and data visualization. The NGS application MethylCap-seq involves the in vitro capture of methylated DNA and subsequent analysis of enriched fragments by massively parallel sequencing. Here, we present a scalable, flexible workflow for MethylCap-seq Quality Control, secondary data analysis, tertiary analysis of multiple experimental groups, and data visualization. This workflow and its suite of features will assist biologists in conducting methylation profiling projects and facilitate meaningful biological interpretation.
AB - Advances in whole genome profiling have revolutionized the cancer research field, but at the same time have raised new bioinformatics challenges. For next generation sequencing (NGS), these include data storage, computational costs, sequence processing and alignment, delineating appropriate statistical measures, and data visualization. The NGS application MethylCap-seq involves the in vitro capture of methylated DNA and subsequent analysis of enriched fragments by massively parallel sequencing. Here, we present a scalable, flexible workflow for MethylCap-seq Quality Control, secondary data analysis, tertiary analysis of multiple experimental groups, and data visualization. This workflow and its suite of features will assist biologists in conducting methylation profiling projects and facilitate meaningful biological interpretation.
KW - Cancer
KW - DNA methylation
KW - Data analysis
KW - Data visualization
KW - Epigenetics
KW - Next generation sequencing
UR - http://www.scopus.com/inward/record.url?scp=84863659766&partnerID=8YFLogxK
U2 - 10.1109/gensips.2011.6169426
DO - 10.1109/gensips.2011.6169426
M3 - Conference contribution
AN - SCOPUS:84863659766
SN - 9781467304900
T3 - Proceedings - IEEE International Workshop on Genomic Signal Processing and Statistics
SP - 1
EP - 4
BT - Proceedings 2011 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS'11
PB - IEEE Computer Society
T2 - 2011 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS'11
Y2 - 4 December 2011 through 6 December 2011
ER -