The views expressed here are those of the individual authors and not necessarily those of the JSM sponsors, their officers, or their staff.
Abstract Details
Activity Number:
|
148
|
Type:
|
Invited
|
Date/Time:
|
Monday, August 1, 2011 : 10:30 AM to 12:20 PM
|
Sponsor:
|
IMS
|
Abstract - #300078 |
Title:
|
Do Multi-Reads Matter in ChIP-Seq Data Analysis?
|
Author(s):
|
Sunduz Keles*+
|
Companies:
|
University of Wisconsin at Madison
|
Address:
|
1300 University Avenue, 1245 MSC, Madison, WI, WI, 53705, USA
|
Keywords:
|
High throughput sequencing ;
ChIP-Seq ;
Mixture models ;
Mappability ;
Transcription factors
|
Abstract:
|
The introduction of next generation sequencing enabled a myriad of creative ways to answer genome-wide questions. In particular, chromatin immunoprecipitation coupled with sequencing (ChIP-Seq) has become a powerful technique for large scale profiling of transcription factor binding and chromatin modifications. A ChIP-Seq experiment generates millions of short reads. The first step of data analysis is to map reads to reference genome and retain reads that map to a single location in the genome (uni-reads). Restraining the analysis to unireads leads to reduced sequencing depth and further poses a significant challenge for identifying binding locations that reside in regions of genome that have been duplicated over evolutionary time.
We investigate the effects of discarding multi-reads in ChIP-Seq data analysis and illustrate that their incorporation can increase sequencing depth up to 20%. We develop a model-based method for taking into account mapping uncertainty in ChIP-Seq data analysis. We quantify and characterize gains from multi-reads in case studies from the ENCODE project, and support our conclusions with both computational and experimental validations.
|
The address information is for the authors that have a + after their name.
Authors who are presenting talks have a * after their name.
Back to the full JSM 2011 program
|
2011 JSM Online Program Home
For information, contact jsm@amstat.org or phone (888) 231-3473.
If you have questions about the Continuing Education program, please contact the Education Department.