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Old 06-14-2011, 10:36 AM   #1
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Thumbs up ChIP seq packages for histone modification data

Hi all,

Which chip seq peak calling algorithm would you suggest to be the best for histone modification data such as H3k4me3, H3k9me3 etc in terms of usage and accuracy.

I am trying to use MACS and cis genome. The peaks donot match (even 10%).
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Old 06-15-2011, 08:35 AM   #2
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what you mean by "peaks donot match"? match what?
are you sure your primary/raw data is any good? what do your eyes tell you when you browse the coverage tracks in a genome browser, do you see an expected pattern?

anyway there are many tools out, none of which has really been tested on a reference dataset that has been independently confirmed with a different technology (afaik). therefore there is no 'best' tool for everybodies dataset.

i personally would tend to recommend SICER as histone modifications are not necessarily found to have peak-shaped enrichment patterns.
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Old 06-16-2011, 10:21 AM   #3
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macs does work for histone modifications, but you have to specify --nomodel. also specify --nolambda if you don't have control data.

they have a workflow in their new publication:
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