PeakSeq: Difference between revisions
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== Software download == | == Software download == | ||
[http://archive.gersteinlab.org/proj/PeakSeq/Scoring_ChIPSeq/Code/C/PeakSeq1.1.tar.bz2 PeakSeq1.1]: 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 PeakSeq1.1]: Re-coded from scratch, runs slightly faster and it is easier to use. Refer to the README file in the archive for help on running PeakSeq. In addition, [ these slides] may be helpful. | ||
Refer to the README file in the archive for help on running PeakSeq. In addition, [ these slides] may be helpful. | |||
[http://archive.gersteinlab.org/proj/PeakSeq/Scoring_ChIPSeq/Code/C/PeakSeq_v1.01.tar.gz PeakSeq1.01]: Original PeakSeq code. | [http://archive.gersteinlab.org/proj/PeakSeq/Scoring_ChIPSeq/Code/C/PeakSeq_v1.01.tar.gz PeakSeq1.01]: Original PeakSeq code. | ||
Revision as of 02:57, 13 July 2011
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
PeakSeq1.1: Re-coded from scratch, runs slightly faster and it is easier to use. Refer to the README file in the archive for help on running PeakSeq. In addition, [ these slides] may be helpful.
PeakSeq1.01: Original PeakSeq code.
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.
