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Old 08-10-2010, 03:50 AM   #1
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Default ChIP-Seq: PeakAnalyzer: Genome-wide annotation of chromatin binding and modification

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PeakAnalyzer: Genome-wide annotation of chromatin binding and modification loci.

BMC Bioinformatics. 2010 Aug 6;11(1):415

Authors: Salmon-Divon M, Dvinge H, Tammoja K, Bertone P

ABSTRACT: BACKGROUND: Functional genomic studies involving high-throughput sequencing and tiling array applications, such as ChIP-seq and ChIP-chip, generate large numbers of experimentally-derived signal peaks across the genome under study. In analyzing these loci to determine their potential regulatory functions, areas of signal enrichment must be considered relative to proximal genes and regulatory elements annotated throughout the target genome. Regions of chromatin association by transcriptional regulators should be distinguished as individual binding sites in order to enhance downstream analyses, such as the identification of known and novel consensus motifs. RESULTS: PeakAnalyzer is a set of high-performance utilities for the automated processing of experimentally-derived peak regions and annotation of genomic loci. The programs can accurately subdivide multimodal regions of signal enrichment into distinct subpeaks corresponding to binding sites or chromatin modifications, retrieve genomic sequences encompassing the computed subpeak summits, and identify positional features of interest such as intersection with exon/intron gene components, proximity to up- or downstream transcriptional start sites and cis-regulatory elements. The software can be configured to run either as a pipeline component for high-throughput analyses, or as a cross-platform desktop application with an intuitive user interface. CONCLUSIONS: PeakAnalyzer comprises a number of utilities essential for ChIP-seq and ChIP-chip data analysis. High-performance implementations are provided for Unix pipeline integration along with a GUI version for interactive use. Source code in C++ and Java is provided, as are native binaries for Linux, Mac OS X and Windows systems.

PMID: 20691053 [PubMed - as supplied by publisher]

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Old 08-24-2012, 08:03 AM   #2
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Default PeakAnnotator PROBLEM

I am trying to annotate peak regions using PeakAnalyzer. I have problems with PeakAnnotator and I get this error message when I try to use the NDG function:

"Files must be sorted by chromosomes,start position, end position"

I tried several times to sort (using either excel or sortBED, still same error message)

I am attaching the files I am currently using: Peak file is "peaks.txt" ( and annotation file (should be chrom, start end-sorted BED) is "annotation.bed" (

Command line used:
> ./PeakAnnotator NDG peaks.txt annotation.bed output

Any suggestions for troubleshooting?
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Old 10-25-2012, 12:08 PM   #3
Mali Salmon
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Hi Eagle_Eye
I just came across your post, and I am wondering if you managed to use PeakAnalyzer. If not I would love to help you out. Just send me the two files (links above don't work) to my personal mail.
Mali (PeakAnalyzer author)
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Old 02-18-2014, 05:42 AM   #4
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Dear Mali,
May I know is it possible to run the PeakAnalyzer as a command line program by providing the input arguments to get the tss annotated tab delimited output file, instead of java GUI.

Originally Posted by Mali Salmon View Post
Hi Eagle_Eye
I just came across your post, and I am wondering if you managed to use PeakAnalyzer. If not I would love to help you out. Just send me the two files (links above don't work) to my personal mail.
Mali (PeakAnalyzer author)
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Old 01-21-2017, 12:50 AM   #5
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Default peakAnalyzer

Please help me...
I want to install peakAnalyzer on command line But I am faced with the following error.

in part of "Go to the PeakAnalyzer directory and launch the program by typing":

"java -jar PeakAnalyzer.jar "&

I am faced with error "org.xml.sax.SAXParseException: lineNumber: 1: clumnNumber: 1: Premature end of file " Please guide me، can I do..


Last edited by rezap222; 01-23-2017 at 05:01 AM.
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