How to visualize Hi-C bed file format?

Question

[mkh]

Hi All,

There is a bed format file for Hi-C data form a supplement of a paper which I would like to visualize it. Is there any software or way that I can use to visualize it? I hope I don't need to do the raw data analysis?

Thanks,

[mkh]

Practically there is two files one is "bin" which looks like:

cbin    chr     from.coord      to.coord        count

1       2L      5000    10000   16

2       2L      10000   15000   34

3       2L      15000   20000   11

4       2L      20000   25000   15

5       2L      25000   30000   26

and the other one is "contact":

cbin1   cbin2   expected_count  observed_count

1       1       0.050971        48

1       2       0.131186        251

1       3       0.051542        95

1       4       0.088498        80

So, could you please tell me how can I combine these file to visualize the target interacting points? Thanks,

Answer 1

[Alex Reynolds]

See: HiGlass and data preparation

Answer 2

[Ian]

It is now possible to view this type of data as a custom track on the UCSC Browser:

http://genome.ucsc.edu/goldenPath/help/interact.html