The DOI matches its Crossref record; 12 of the 12 references it cites were found in a registry or an index.
Computation for ChIP-seq and RNA-seq studies
Open accessAbstract
Genome-wide measurements of protein-DNA interactions and transcriptomes are increasingly done by deep DNA sequencing methods (ChIP-seq and RNA-seq). The power and richness of these counting-based measurements comes at the cost of routinely handling tens to hundreds of millions of reads. Whereas early adopters necessarily developed their own custom computer code to analyze the first ChIP-seq and RNA-seq datasets, a new generation of more sophisticated algorithms and software tools are emerging to assist in the analysis phase of these projects. Here we describe the multilayered analyses of ChIP-seq and RNA-seq datasets, discuss the software packages currently available to perform tasks at each layer and describe some upcoming challenges and features for future analysis tools. We also discuss how software choices and uses are affected by specific aspects of the underlying biology and data structure, including genome size, positional clustering of transcription factor binding sites, transcript discovery and expression quantification.
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Cites
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Self-citationHigh-Resolution Profiling of Histone Methylations in the Human Genome
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“The RNA sequences themselves can be mined to identify positions where the base reported differs from the reference genome(s), identifying either a single-nucleotide polymorphism or a private mutation 25,43 .”
Background
Cited by
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al. (2010) · Genome Research · doi:10.1101/gr.107524.110 · Cited by 27,895
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Self-citationEnrichr: interactive and collaborative HTML5 gene list enrichment analysis tool
Chen, E. Y., Tan, C. M., Kou, Y., Duan, Q., Wang, Z., Meirelles, G. V., Clark, N. R., & Ma’ayan, A. (2013) · BMC Bioinformatics · doi:10.1186/1471-2105-14-128 · Cited by 7,814
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
Landt, S. G., Marinov, G. K., Kundaje, A., Kheradpour, P., Pauli, F., Batzoglou, S., Bernstein, B. E., Bickel, P., Brown, J. B., Cayting, P., et al. (2012) · Genome Research · doi:10.1101/gr.136184.111 · Cited by 2,033
Self-citationEpigenetics and the environment: emerging patterns and implications
Feil, R., & Fraga, M. F. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3142 · Cited by 1,929
Metadata
- Authors
- Pepke, S., Wold, B., & Mortazavi, A.
- Venue
- Nature Methods
- Published
- 2009-10-15
- Volume
- 6
- Issue
- S11
- Pages
- S22-S32
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W1968475238
- Cited by
- 557
- References
- 12
- FWCI
- 26.89
- Type
- journal article
- Language
- en
- Open access
- green
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