How is this generated? macs2_peaks_final.replicated.narrowPeak

[YichaoOU]

For the narrowPeak file, is it just using common MACS2 parameters for TF or histones?

I mean, do I first need to treat the HiChIP data as a paired-end chip-seq data and do peak calling? and then use the narrowpeak file for this hichip pipeline?

Thanks, Yichao

[ijuric]

So, you need to have .narrowpeak file to run MAPS. How you obtain it is a different issue which will depend on many things. We usually run MACS2 on chipseq data to call peaks, but sometimes you might be lucky and work with cell types that someone else used before and there is a good list of 1D peaks in the literature. I hope this helps. Ivan

On Mon, Aug 26, 2019 at 2:11 PM Yichao Li notifications@github.com wrote:

For the narrowPeak file, is it just using common MACS2 parameters for TF or histones?

I mean, do I first need to treat the HiChIP data as a paired-end chip-seq data and do peak calling? and then use the narrowpeak file for this hichip pipeline?

Thanks, Yichao

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[YichaoOU]

Got it. If I understand your paper correctly, mango and hichipper only identify interactions bases on these anchor regions and your program can identify interactions outside the given regions. But still, one of the two interacting regions should be in the anchor list, right?

Thanks, Yichao

[armenabnousi]

yes, that's correct!