searching tool for ChIP-seq analysis of histone modification analysis

[tujchl]

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!

[kopi-o]

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.

[tujchl]

Got it! thanks kopi-o, I am gonna try them all

[lshen]

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.

[gene_x]

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!

[crazyhottommy]

I would recommend http://cistrome.dfci.harvard.edu/Cis...e_Project.html
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