PeakSeq
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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 == | ||
| - | Rozowsky | + | 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 | + | |
== Software download == | == Software download == | ||
| - | [http://archive.gersteinlab.org/proj/PeakSeq/Scoring_ChIPSeq/Code/C/ | + | [http://archive.gersteinlab.org/proj/PeakSeq/Scoring_ChIPSeq/Code/C/PeakSeq_1.31.zip PeakSeq version 1.31]: Bug fix for preprocessing. |
| - | + | [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. | |
| - | [http://archive.gersteinlab.org/proj/PeakSeq/Scoring_ChIPSeq/Code/C/PeakSeq_v1.01.tar.gz | + | [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 == | ||
| - | + | Mapability maps for several organisms can be found [http://archive.gersteinlab.org/proj/PeakSeq/Mappability_Map/ here] | |
| - | + | === 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.
