need examples, epic2, epic2-bw, epic2-df

[YichaoOU]

I think epic2 is for regular peak calling (e.g., TF-chip vs. input)? epic2-df is for differential peak calling (treatment vs. control)? Then what is epic2-bw for?

Thanks, Yichao

[endrebak]

Epic2: ChIP vs input Epic2-df : ChIP from condition1 vs chip from condition2 (eg tumor vs normal) Epic2-bw: create bigwigs of your data for visualization in genome browsers.

Great question. I should clarify this in the readme for noobs. I forget that it is not obvious for those not familiar with the original SICER.

On Thursday, June 6, 2019, Yichao Li [email protected] wrote:

I think epic2 is for regular peak calling (e.g., TF-chip vs. input)? epic2-df is for differential peak calling (treatment vs. control)? Then what is epic2-bw for?

Thanks, Yichao

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[crazyhottommy]

Hi, The FDR for Epic2-df is confusing to me. why there are two FDRs for the same region? if a region is down with an FDR 0.05 comparing KO to WT. it should be up with the same FDR comparing WT to KO?

Thanks for epic2, it is very good for calling diffuse domains.

[endrebak]

epic2-df, like SICER-df, uses a poisson distribution for computing the p-values, using KO as an average/lambda for WT and vice versa.

[endrebak]

I actually do not understand the epic2-df statistics well, I only ensured that epic2-df produced the same results as SICER-df.

[crazyhottommy]

okay. thanks for answering.