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...
| Main Authors: | , , , , , |
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| Other Authors: | |
| Format: | Article |
| Language: | English |
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BioMed Central
2015
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| Online Access: | http://hdl.handle.net/1721.1/98902 https://orcid.org/0000-0002-3430-6943 |
| _version_ | 1826210871952539648 |
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| author | He, Xin Cicek, A. Ercument Wang, Yuhao Schulz, Marcel H. Le, Hai-Son Bar-Joseph, Ziv |
| author2 | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory |
| author_facet | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory He, Xin Cicek, A. Ercument Wang, Yuhao Schulz, Marcel H. Le, Hai-Son Bar-Joseph, Ziv |
| author_sort | He, Xin |
| collection | MIT |
| description | 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. |
| first_indexed | 2024-09-23T14:56:48Z |
| format | Article |
| id | mit-1721.1/98902 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T14:56:48Z |
| publishDate | 2015 |
| publisher | BioMed Central |
| record_format | dspace |
| spelling | mit-1721.1/989022022-09-29T11:34:55Z De novo ChIP-seq analysis He, Xin Cicek, A. Ercument Wang, Yuhao Schulz, Marcel H. Le, Hai-Son Bar-Joseph, Ziv Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science Wang, Yuhao 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. 2015-09-24T17:52:22Z 2015-09-24T17:52:22Z 2015-09 2015-06 2015-09-24T03:41:56Z Article http://purl.org/eprint/type/JournalArticle 1474-760X http://hdl.handle.net/1721.1/98902 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. https://orcid.org/0000-0002-3430-6943 en http://dx.doi.org/10.1186/s13059-015-0756-4 Genome Biology He et al. application/pdf BioMed Central |
| spellingShingle | He, Xin Cicek, A. Ercument Wang, Yuhao Schulz, Marcel H. Le, Hai-Son Bar-Joseph, Ziv De novo ChIP-seq analysis |
| title | De novo ChIP-seq analysis |
| title_full | De novo ChIP-seq analysis |
| title_fullStr | De novo ChIP-seq analysis |
| title_full_unstemmed | De novo ChIP-seq analysis |
| title_short | De novo ChIP-seq analysis |
| title_sort | de novo chip seq analysis |
| url | http://hdl.handle.net/1721.1/98902 https://orcid.org/0000-0002-3430-6943 |
| work_keys_str_mv | AT hexin denovochipseqanalysis AT cicekaercument denovochipseqanalysis AT wangyuhao denovochipseqanalysis AT schulzmarcelh denovochipseqanalysis AT lehaison denovochipseqanalysis AT barjosephziv denovochipseqanalysis |