Tools to calculate directionality index

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5.2 years ago

h.long ▴ 40

Hi,

I am looking for a software tool which will allow me to use the directionality index to call TADs as defined by Dixon et al. 2012. I found a tool called Domain caller which I believe has been created by the authors of the paper, however Rao et al. 2014 used this tool in the supplementary methods of their paper and found that when using higher resolution data it failed on some chromosomes.

Since I want to use higher resolution data I am now looking into using a function from the R package HiTC. In order to use this I would need to convert .hic files (the format produced by Juicer) to a HTClist object.

Does anyone know how to do this? or does anyone know of any other tools implementing directionality index?

Thank you!

R next-gen • 1.5k views

ADD COMMENT • link updated 4.0 years ago by Ljs • 0 • written 5.2 years ago by h.long ▴ 40

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I have the same question.Do you resolve it ?

ADD REPLY • link 4.0 years ago by Ljs • 0

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HiTC is a package that needs contact maps to be converted to HiC-Pro format. It is possible to convert HiC-Pro maps to .hic files, but not vice-versa AFAIK. To be able to use HiTC, I needed to run HiC-Pro first and use the resulting maps as input.

As an alternative, you can try FAN-C.

ADD REPLY • link 3.4 years ago by chorzoww • 0

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