PeakSeq
From GersteinInfo
(→Software download) |
(→Citation) |
||
| Line 3: | Line 3: | ||
== Citation == | == Citation == | ||
| - | Rozowsky J, Euskirchen G, Auerbach R, Zhang Z, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein M | + | PeakSeq algorithm is described in: Rozowsky J, Euskirchen G, Auerbach R, Zhang Z, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein M |
| - | + | ||
Nature Biotechnology 27, 66 - 75 (2009). | Nature Biotechnology 27, 66 - 75 (2009). | ||
Revision as of 19:43, 19 July 2011
PeakSeq is a program for identifying and ranking peak regions in ChIP-Seq experiments. It takes as input, mapped reads from a ChIP-Seq experiment, mapped reads from a control experiment and outputs a file with peak regions ranked with increasing Q-values.
Contents |
Citation
PeakSeq algorithm is described in: Rozowsky J, Euskirchen G, Auerbach R, Zhang Z, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein M Nature Biotechnology 27, 66 - 75 (2009).
Software download
PeakSeq version 1.1: Re-coded from scratch, runs slightly faster and it is easier to use, and supports multiple mapped read file formats. Refer to the README file in the archive for help on running PeakSeq. In addition, these slides may be helpful.
PeakSeq version 1.01: Original PeakSeq code.
Additional Resources Related to PeakSeq
Mapability maps for several organisms can be found here
Datasets
Raw ChIP-Seq Sequence Data: PolII, STAT-1
Yale Chip-seq Data Pipeline
Illumina pipeline (wrapper for Illumina pipeline)
Chip-seq scoring pipeline (runs PeakSeq)
Also, one might want to consider ChipSeqSim : http://papers.gersteinlab.org/papers/chip-seq-simu/
Contact
Joel Rozowsky at joel DOT rozowsky AT yale DOT edu or Arif Harmanci at Arif DOT Harmanci AT yale DOT edu.
