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vaquerizaslab / tadtool

TADtool is an interactive tool for the identification of meaningful parameters in TAD-calling algorithms for Hi-C data.
MIT License
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Raw or Iced matrices as input? #20

Closed rikrdo89 closed 5 years ago

rikrdo89 commented 5 years ago

Hi, this is a question rather than an issue, but I wasn't able to find anything in the documentation regarding the type of matrix that would work better for identifying TADs using TADtool. I have both raw and iced matrixes from HiC-pro pipeline. I suppose Iced matrices would be better since they are already normalized, but I want to make sure this is the case. Thank you.

kaukrise commented 5 years ago

Yes, use ICE-normalised matrices whenever possible. TADtool will also work on raw counts matrices, but the TAD calls will be less affected by biases when using normalised input!

On Thu, Oct 17, 2019 at 3:51 AM rikrdo89 notifications@github.com wrote:

Hi, this is a question rather than an issue, but I wasn't able to find anything in the documentation regarding the type of matrix that would work better for identifying TADs using TADtool. I have both raw and iced matrixes from HiC-pro pipeline. I suppose Iced matrices would be better since they are already normalized, but I want to make sure this is the case. Thank you.

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rikrdo89 commented 5 years ago

That's what I thought. Thank you! I have one more question/issue when loading matrices and bed files straight from HiC-pro... I get an error re: "file cannot contain pickled data". I'll open a new issue.