PeakSeq

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= 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.
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 ==
== Citation ==
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Rozowsky J, Euskirchen G, Auerbach R, Zhang Z, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein M
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PeakSeq is described in Rozowsky et al. <i>Nature Biotech</i> 27: 66 ([http://papers.gersteinlab.org/papers/PeakSeq more])
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Nature Biotechnology 27, 66 - 75 (2009).
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== Software download ==
== Software download ==
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[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.
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[http://archive.gersteinlab.org/proj/PeakSeq/Scoring_ChIPSeq/Code/C/PeakSeq_1.31.zip PeakSeq version 1.31]: Bug fix for preprocessing.
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[http://archive.gersteinlab.org/proj/PeakSeq/Scoring_ChIPSeq/Code/C/PeakSeq_v1.01.tar.gz PeakSeq1.01]: Original PeakSeq code.
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[http://archive.gersteinlab.org/proj/PeakSeq/Scoring_ChIPSeq/Code/C/PeakSeq.zip PeakSeq version 1.3]: Several bug fixes, cleanup of the command line while PeakSeq runs.
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[http://archive.gersteinlab.org/proj/PeakSeq/Scoring_ChIPSeq/Code/C/PeakSeq.v1.1.tar.bz2 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, [http://archive.gersteinlab.org/proj/PeakSeq/peakseq_v.1.1.ppt these slides] may be helpful.
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[http://archive.gersteinlab.org/proj/PeakSeq/Scoring_ChIPSeq/Code/C/PeakSeq_v1.01.tar.gz PeakSeq version 1.01]: Original PeakSeq code.
== Additional Resources Related to PeakSeq ==
== Additional Resources Related to PeakSeq ==
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=== Yale Chip-seq Data Pipeline ===
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Mapability maps for several organisms can be found [http://archive.gersteinlab.org/proj/PeakSeq/Mappability_Map/ here]
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Software download
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=== Datasets ===
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Raw ChIP-Seq Sequence Data: [http://archive.gersteinlab.org/proj/PeakSeq/Sequence_Data/HeLa-S3 PolII], [http://archive.gersteinlab.org/proj/PeakSeq/Sequence_Data/Stimulated_HeLa-S3 STAT-1]
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=== Yale Chip-seq Data Pipeline ===
[http://array.mbb.yale.edu/pipeline/illumina.html Illumina pipeline] (wrapper for Illumina pipeline)
[http://array.mbb.yale.edu/pipeline/illumina.html Illumina pipeline] (wrapper for Illumina pipeline)

Latest revision as of 17:21, 2 March 2015

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 is described in Rozowsky et al. Nature Biotech 27: 66 (more)

Software download

PeakSeq version 1.31: Bug fix for preprocessing.

PeakSeq version 1.3: Several bug fixes, cleanup of the command line while PeakSeq runs.

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.

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