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Old 10-21-2009, 08:47 PM   #1
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Location: san fran

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Default Any program to extract different peaks from two wigs files

Hi, after running peak search program on my ChIP-seq data I got wig files which I can view in UCSC genome browser. The next level analysis is two extract the difference between two wig files from two ChIP-seq samples. Anyone knows this kind of program or codes. Please kindly tell me. A lot of thanks!
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Old 10-29-2009, 01:30 AM   #2
Location: Manchester, UK

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You can generate a BED file of the binding sites of each sample. Then using overlapSelect from Jim Kents source tree you can generate a file with the overlapping regions. Then just with some simple scripting you can achieve your task. PM me if you need more details

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