Comparison of ChIP-seq tracks from two cell lines using FC over control (ENCODE data)

Question

[erica.fary]

Hi everyone,

I would like to compare H3K27ac ChIP-seq data at a specific genomic interval between 2 cell lines but I am a newbie in ChIP-seq... My plan is simply to proceed as follows:

• download from ENCODE the rep1,2 bigWig files containing fold-change (FC) over control (1 file per cell line)
• convert bigWig to bedGraph
• boxplot of the values that fall within the genomic interval of interest (1 box per cell line)

My questions are the following:

• is it correct to directly compare FC values across cell lines ? (my impression is that this provides a kind of normalization and makes the cell lines comparable, by I could not find a clear answer)
• is it better to use rep1,2 file or to pool the rep1 and rep2 files ?
• would it be better to compare cell lines using peaks BED data or signal values or signal p-values ? with what kind of normalization then to make data comparable across cell lines ?
• or otherwise how would you have conducted this analysis ?

any help would be appreciated :)

Thanks