Title |
SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing
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Published in |
Bioinformatics, June 2012
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DOI | 10.1093/bioinformatics/bts337 |
Pubmed ID | |
Authors |
Zhifu Sun, Saurabh Baheti, Sumit Middha, Rahul Kanwar, Yuji Zhang, Xing Li, Andreas S. Beutler, Eric Klee, Yan W. Asmann, E. Aubrey Thompson, Jean-Pierre A. Kocher |
Abstract |
Reduced representation bisulfite sequencing (RRBS) is a cost-effective approach for genome-wide methylation pattern profiling. Analyzing RRBS sequencing data is challenging and specialized alignment/mapping programs are needed. Although such programs have been developed, a comprehensive solution that provides researchers with good quality and analyzable data is still lacking. To address this need, we have developed a Streamlined Analysis and Annotation Pipeline for RRBS data (SAAP-RRBS) that integrates read quality assessment/clean-up, alignment, methylation data extraction, annotation, reporting and visualization. This package facilitates a rapid transition from sequencing reads to a fully annotated CpG methylation report to biological interpretation. |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
Montenegro | 1 | 50% |
Unknown | 1 | 50% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Scientists | 2 | 100% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Brazil | 2 | 2% |
United States | 2 | 2% |
India | 2 | 2% |
Switzerland | 1 | 1% |
Germany | 1 | 1% |
Unknown | 92 | 92% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 27 | 27% |
Student > Ph. D. Student | 24 | 24% |
Student > Master | 14 | 14% |
Professor > Associate Professor | 6 | 6% |
Student > Bachelor | 6 | 6% |
Other | 15 | 15% |
Unknown | 8 | 8% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 40 | 40% |
Biochemistry, Genetics and Molecular Biology | 20 | 20% |
Computer Science | 9 | 9% |
Medicine and Dentistry | 5 | 5% |
Neuroscience | 4 | 4% |
Other | 13 | 13% |
Unknown | 9 | 9% |