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Old 09-28-2010, 09:41 PM   #1
honey
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Default chip seq peaks on whole genome

I am having list of peaks corresponding to human genome and would like to have them mapped to whole human genome how can do that, Most of visulaization tool provide on eor two chromomes analysis at a time.
Any advise please
Thanks
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Old 09-29-2010, 08:50 AM   #2
mattanswers
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Use SeqMonk,
http://www.bioinformatics.bbsrc.ac.uk/projects/seqmonk/

You will also need a few Gb of RAM and you can adjust SeqMonk as to how much memory it is allowed to use.
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Old 09-29-2010, 12:46 PM   #3
jjw14
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I second the recommendation for SeqMonk. Very flexible options to analyze peak data. The author of the program posts regularly in the SeqAnswers forums and is really helpful.
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Old 09-29-2010, 01:46 PM   #4
honey
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Thanks for your help. Will it allow me visualization of whole geneome binding sites that is include track on all chromosomes at teh same time
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Old 09-29-2010, 02:05 PM   #5
mattanswers
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You can have all the chromosomes open (as in the attached image), but to look for binding sites then you can only see one chromosome at a time (the bottom half of the image). However, you can very easily switch between chromosomes by just clicking on a particular chromosome to see it.

From a post elsewhere on this site (http://seqanswers.com/forums/showthread.php?t=7047), the author of SeqMonk indicated that the next version will allow you to see binding sites on all chromosomes at one time. Go to the above URL and scroll about half-way down the page to see an example.
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File Type: jpg SeqMonk.jpg (67.3 KB, 11 views)
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