De novo ChIP-seq analysis
Name
13059_2015_Article_756.pdf
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1.49 MB
Format
Adobe PDF
Checksum (MD5)
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Author(s)
He, Xin
Cicek, A. Ercument
Wang, Yuhao
Schulz, Marcel H.
Le, Hai-Son
Bar-Joseph, Ziv
Date Issued
September 2015
Journal
Genome Biology
Publisher
BioMed Central
Citation
He, Xin, A. Ercument Cicek, Yuhao Wang, Marcel H. Schulz, Hai-Son Le, and Ziv Bar-Joseph. "De novo ChIP-seq analysis." Genome Biology. 2015 Sep 23;16(1):205.
Version
Final published version
Abstract
Methods for the analysis of chromatin immunoprecipitation sequencing (ChIP-seq) data start by aligning the short reads to a reference genome. While often successful, they are not appropriate for cases where a reference genome is not available. Here we develop methods for de novo analysis of ChIP-seq data. Our methods combine de novo assembly with statistical tests enabling motif discovery without the use of a reference genome. We validate the performance of our method using human and mouse data. Analysis of fly data indicates that our method outperforms alignment based methods that utilize closely related species.
MIT Department
Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science
Persistent DSpace Link
DOI of Published Version
https://doi.org/10.1186/s13059-015-0756-4
