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Old 03-08-2010, 03:45 AM   #1

Join Date: Sep 2009
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Default searching tool for ChIP-seq analysis of histone modification analysis

hi folks:
I want to analyze chip-seq data of histone modification, and I search some related tools such as QuEST, peakseq as well as some reviews on this topic and found tool for histone is lacking or weak at least.
so could somebody recommand a suitable tool for histone for me?

thanks in advanced!
tujchl is offline   Reply With Quote
Old 03-08-2010, 04:49 AM   #2
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There aren't many tools for this particular application. You could try SICER or CCAT (run the latter in "region mode"). These tools have been used for finding regions enriched in histone modifications.
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Old 03-09-2010, 01:20 AM   #3

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Got it! thanks kopi-o, I am gonna try them all
tujchl is offline   Reply With Quote
Old 06-16-2010, 12:21 PM   #4
Location: Toronto

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Any one had experience comparing SICER and CCAT? I have a data set that returned >1000 peaks H3K27me3 in SICER default setting (FDR 1e-3), but no peaks in CCAT. This data set seems poorly enriched in CHIP step. But still want to pull out some reliable peaks from it.
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Old 02-22-2013, 05:45 AM   #5
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We wrote scripts to calculate coverage (RPKM etc) of certain bin length using histone ChIP-seq data. histone data is a lot more sparse than transcription factor ChIP-seq. Maybe a good place to start is to look at those high profile papers such as ENCODE and see how they handle their histone ChIP-seq.

Good luck!
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Old 03-13-2013, 10:00 AM   #6
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I would recommend
Cistrome is developed by Xiaole Shirley Liu Lab in Harvard
It is Galaxy based and you do not need any programming skills to use it
crazyhottommy is offline   Reply With Quote

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