I have two chip-seq experiments under two conditions. I was wondering if it was possible to say that a peak is 'bigger' in one condition versus the other and if there is software that will quantify the difference. Current chip-seq peak callers seem to just say if there is a peak or not.
Thanks
5 answers
One option is to use DESeq to analyse count data from the Chip-seq summits in your two conditions and test for differential intensity:
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Thanks, I will give DESeq a try,
I have found a paper that seems to address this issue but approaches it in an entirely different way
"Identifying dispersed epigenomic domains from ChIP-Seq data." http://www.ncbi.nlm.nih.gov/pubmed/21325299
Their software RSEG can be found here: http://smithlab.cmb.usc.edu/histone/rseg/
Also SICER. Rseg runs slower than SICER. You may want to use ChIPDiff which uses HMM and could be fed the output -island.bed files. You can tune confidence% and "fold change" parameters to solve your problem.
Bailey T, Krajewski P, Ladunga I, Lefebvre C, Li Q, et al. (2013) Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data. PLoS Comput Biol 9(11): e1003326. doi:10.1371/journal.pcbi.1003326
http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003326
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