PeakSeq
From GersteinInfo
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| - | = Additional Resources Related to PeakSeq = | + | = PeakSeq: Systematic Scoring of ChIP-Seq Experiments Relative to Controls = |
| + | 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. | ||
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| + | == Citation == | ||
| + | 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 == | ||
| + | Version 1.1: Re-coded from scratch, runs slightly faster and it is easier to use. | ||
| + | |||
| + | http://archive.gersteinlab.org/proj/PeakSeq/Scoring_ChIPSeq/Code/C/PeakSeq1.1.tar.bz2 | ||
| + | |||
| + | Refer to the README file in the archive for help on running PeakSeq. In addition, [ these slides] may be helpful. | ||
| + | |||
| + | Version 1.0.1: | ||
| + | |||
| + | http://archive.gersteinlab.org/proj/PeakSeq/Scoring_ChIPSeq/Code/C/PeakSeq_v1.01.tar.gz | ||
| + | |||
| + | == Additional Resources Related to PeakSeq == | ||
=== Yale Chip-seq Data Pipeline === | === Yale Chip-seq Data Pipeline === | ||
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Also, one might want to consider ChipSeqSim : http://papers.gersteinlab.org/papers/chip-seq-simu/ | 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. | + | == Contact == |
| + | Joel Rozowsky at joel DOT rozowsky AT yale DOT edu or Arif Harmanci at Arif DOT Harmanci AT yale DOT edu. | ||
Revision as of 02:54, 13 July 2011
Contents |
PeakSeq: Systematic Scoring of ChIP-Seq Experiments Relative to Controls
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.
Citation
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
Version 1.1: Re-coded from scratch, runs slightly faster and it is easier to use.
http://archive.gersteinlab.org/proj/PeakSeq/Scoring_ChIPSeq/Code/C/PeakSeq1.1.tar.bz2
Refer to the README file in the archive for help on running PeakSeq. In addition, [ these slides] may be helpful.
Version 1.0.1:
http://archive.gersteinlab.org/proj/PeakSeq/Scoring_ChIPSeq/Code/C/PeakSeq_v1.01.tar.gz
Additional Resources Related to PeakSeq
Yale Chip-seq Data Pipeline
Software download
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.
