Cargando…

De novo ChIP-seq analysis

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...

Descripción completa

Detalles Bibliográficos
Autores principales: He, Xin, Cicek, A. Ercument, Wang, Yuhao, Schulz, Marcel H., Le, Hai-Son, Bar-Joseph, Ziv
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4579611/
https://www.ncbi.nlm.nih.gov/pubmed/26400819
http://dx.doi.org/10.1186/s13059-015-0756-4
Descripción
Sumario: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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-015-0756-4) contains supplementary material, which is available to authorized users.