Question: How to use Hi-C data?
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gravatar for framtid1994
8 months ago by
framtid19940 wrote:

Hi

Im very new to Hi-C and Im not quite sure how to approach these data, as they look a bit stranger than Im used to from e.g. ChIA-PET data. In ChIA-PET data you get the regions that are interacting, but all the Hi-C data I have seen so far is presented like this (after raw sequencing data have been processed by e.g. HiC-pro):

HWI-D00119:283:HVWGBCXX:2:2113:7308:28159 chr1 10032 - chr13 47215551 -
HWI-D00119:284:HVWGBCXX:2:2205:16386:19423 chr1 10035 - chr7 13791889 -

As I understand this data position 10032 at chr1 interacts with 47215551 at chr13, but shouldnt it be regions instead for interaction start and interaction end instead of a specific position?

E.g. chr1 10032 10050 chr13 47215551 47215600

Is the position from the Hi-C where the biotin-labeled nucleotide is found on each restriction fragment?

Is there any way to convert these data into bed files displaying these interactions? What I very much would like to do with these data is to see whether my list of CpGs in one interacting end is forming interaction with a gene in the other end.

Thanks in advance!

sequencing next-gen genome • 284 views
ADD COMMENTlink modified 7 months ago by geek_y11k • written 8 months ago by framtid19940
0
gravatar for geek_y
7 months ago by
geek_y11k
Barcelona
geek_y11k wrote:

Its too late to answer but may be useful to others.

They are just the position of reads (ValidPairs) of a ligated fragment. They can not be considered as a real "interactions" unless you call statistically significant interactions. Usually the genome is binned (5KB, 10KB etc ) and then the reads are overlapping each bin are counted and which undergoes a statistical testing. Hi-C is not at basepair resolution , so its always a window which depends on the approximate resolution of the data.

Hi-C pro also has hicpro2juicebox.sh for Juicebox compatibility

ADD COMMENTlink modified 7 months ago • written 7 months ago by geek_y11k
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