enough confident interactions to learn the model about chia-pet2 HOT 3 CLOSED

Hi Rayezh,

The command you used seems appropriate to me. From the QC plot, I'm not sure whether the quality of this dataset is good enough to do sequential analysis. You probably notice that the duplicate rate is very high and the inter/intra ratio is also high. What's the karyotype of this cell line? If there are many chromosome structure variations, the interchromosomal portion will be high.

Or do you find any published paper that used this dataset ?

Guipeng

from chia-pet2.

Actually this dataset was published in this paper:
Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation
the karyotype was normal as diploid as they discribed and they used ChIA-PET Tool to call the peaks although the specific process was not described very much detailed in the paper. I'm trying to replicated their peak calling procedure but failed.
I wonder if there're some critical differeces between CPT and CPT2 that might be overlooked?

from chia-pet2.

And I just checked their processed interactions uploaded in ENCODE(https://www.encodeproject.org/files/ENCFF001THT/) and found their interactions are indeed mostly interchromosome and only a small fraction of them are intrachromosome(605/10762). It should be their data's problem.

Thanks for your help!

from chia-pet2.