- AutorIn
- Lydia Müller
- Daniel Gerighausen
- Mariam Farman
- Dirk Zeckzer
- Titel
- Sierra platinum
- Untertitel
- a fast and robust peak-caller for replicated ChIP-seq experiments with visual quality-control and -steering
- Zitierfähige Url:
- https://nbn-resolving.org/urn:nbn:de:bsz:15-qucosa-216471
- Quellenangabe
- BMC Bioinformatics (2016) 17:377 DOI 10.1186/s12859-016-1248-6
- Erstveröffentlichung
- 2016
- Abstract (EN)
- Background: Histone modifications play an important role in gene regulation. Their genomic locations are of great interest. Usually, the location is measured by ChIP-seq and analyzed with a peak-caller. Replicated ChIP-seq experiments become more and more available. However, their analysis is based on single-experiment peak-calling or on tools like PePr which allows peak-calling of replicates but whose underlying model might not be suitable for the conditions under which the experiments are performed. Results: We propose a new peak-caller called \"Sierra Platinum\" that allows peak-calling of replicated ChIP-seq experiments. Moreover, it provides a variety of quality measures together with integrated visualizations supporting the assessment of the replicates and the resulting peaks, as well as steering the peak-calling process. Conclusion: We show that Sierra Platinum outperforms currently available methods using a newly generated benchmark data set and using real data from the NIH Roadmap Epigenomics Project. It is robust against noisy replicates.
- Andere Ausgabe
- Link zur Originalpublikation in der Zeitschrift BMC Bioinformatics
Link: http://dx.doi.org/10.1186/s12859-016-1248-6 - Freie Schlagwörter (DE)
- ChIP-Seq, Histonmodifikation, Replikation
- Freie Schlagwörter (EN)
- ChIP-seq, Chromatin ImmunoPrecipitation DNA-Sequencing, peak-caller, histone modifications, replicate analysis
- Klassifikation (DDC)
- 530
- 004
- Herausgeber (Institution)
- Universität Leipzig
- Verlag
- BioMed Central, London
- URN Qucosa
- urn:nbn:de:bsz:15-qucosa-216471
- Veröffentlichungsdatum Qucosa
- 19.12.2016
- Dokumenttyp
- Artikel
- Sprache des Dokumentes
- Englisch