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Old 05-08-2012, 01:38 AM   #1
john789
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Location: England

Join Date: Jan 2011
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Default narrowpeak data from wig files?

Hi

I've downloaded some chip-seq data from geo (http://www.ncbi.nlm.nih.gov/geo/) and the only option is .wig format. I'd like the data in an 'ENCODE narrowPeak' style; i.e. something like

Quote:
chromosome start stop strand score p-value
The original paper used macs for peak finding but it seems wig files are output from this tool not input! Can anyone tell me how to get .wig data into a peak list format I can make use of?

Many thanks
John
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Old 08-28-2013, 01:13 AM   #2
pmad
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Location: University of Cambridge, UK

Join Date: Jun 2010
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Default Narrow peaks in ChIP-seq WIG files

Hi John,

The Bioconductor package NarrowPeaks

http://bioconductor.org/packages/rel...rrowPeaks.html

is able to do what you mention. It takes a WIG files and analyzes the shape of candidate regions over a continuum to identify narrow peaks.


Best,
P
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