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RegulatoryGenomicsGroup / chicdiff

A differential caller for capture Hi-C data
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multiple designDir for chicdiff? #14

Open aturocks opened 2 years ago

aturocks commented 2 years ago

Hello,

I have performed cHiC experiments for the same set of baits in both human and chimpanzee samples (and each species has its own rmap/ baitmap file because of different DpnII digestion sites). Does Chicdiff allow for multiple Designdir folders to find differential interactions between human and chimp?

mspivakov commented 2 years ago

Hello! Unfortunately no, it requires exactly the same design for both experiments.

On Fri, 28 Oct 2022, 20:36 aturocks, @.***> wrote:

Hello,

I have performed cHiC experiments for the same set of baits in both human and chimpanzee samples (and each species has its own rmap/ baitmap file because of different DpnII digestion sites). Does Chicdiff allow for multiple Designdir folders to find differential interactions between human and chimp?

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aturocks commented 2 years ago

Hi Michael,

Ah, I see. Thanks for the prompt reply anyway!

Do you have any suggestions for tools/ stat packages which could be used to systematically find cross species differential interactions?

mspivakov commented 2 years ago

I think you'll probably need to map them to some common joint reference (however imperfectly) before they can be compared. But I'm not an expert - perhaps check papers from Paul Flicek and Duncan Odom for some ideas.

On Fri, 28 Oct 2022 at 20:44, aturocks @.***> wrote:

Hi Michael,

Ah, I see. Thanks for the prompt reply anyway!

Do you have any suggestions for tools/ stat packages which could be used to analyze such cross species differential interactions?

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aturocks commented 2 years ago

Thanks for the info, Michael!