ChIP seq packages for histone modification data

[anagari]

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%).

[mudshark]

hi.

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.

[jbrwn]

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: http://goo.gl/5HQlO