Question: Decent random controls for a group of specific ChIP-seq peaks with respect to nucleosome occupancy
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gravatar for AlicePsyche
19 months ago by
AlicePsyche30
United Kingdom
AlicePsyche30 wrote:

Hi, all

I have a group of specific H3K27ac ChIP-seq peaks. I want to generate corresponding random control regions and then do some comparison. It seems that bedtools shuffle is a general way to do this. But I think the decent random control should be located in regions with relatively high nucleosome occupancy. I happened to have a very high-resolution H3 ChIP-seq data(enough to detect 1bp nucleosome phasing...). The problem is that I do not know how to get the "H3-depleted" regions (used as mask regions in bedtools shuffle). Calling peaks is not an option (H3 ChIP is flat)

Is it the right way to do this? Could you please give me some guidance?

sequencing chip-seq genome • 428 views
ADD COMMENTlink modified 19 months ago • written 19 months ago by AlicePsyche30
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