Does anyone know of a tool for analysing 4Cseq (experiment with single cutter)?

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Wen-Ching Chan

you might try this one http://compgenomics.weizmann.ac.il/tanay/?page_id=367

Shruti Sinha

Thank you for the suggestion,

I have checked their method and it requires two cutters.

I tried running the program with single cutter, but it doesn't work. No figures are generated and the nearcis.cover.txt files has NAs .

Hi Shruti Sinha, did you try to look for corresponding softwares listed there

http://omictools.com/3c-4c-5c-hi-c-chia-pet-c298-p1.html

Meanwhile, I thought the canonical 4C experiment always uses different cutter for each digestion. Sorry for the naive question.

Hi Wen-Ching Chan,

Yes, normally there are two different cutters. However, we had to modify the protocol due to the complex region we are focussing on.

Thanks for the link, I have checked it before, but couldn't find any tool for my usage. Will have a thorough check at it again, in case I missed something.