visualize Hi-C .cool file in R

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5.8 years ago

ta_awwad ▴ 340

Hello everyone,

I am really new in visualising Hi-C data. Now I have normalized .cool files and I would like to visiualize it in R using HiTC package .. my .cool files are in the following format:

chrom1    start1    end1    chrom2    start2    end2    count    balanced

chr18    10500000    10600000    chr18    10500000    10600000    1163    0.0482848

chr18    10500000    10600000    chr18    10600000    10700000    574    0.0397891

chr18    10500000    10600000    chr18    10700000    10800000    588    0.0312273

chr18    10500000    10600000    chr18    10800000    10900000    602    0.0255296

chr18    10500000    10600000    chr18    10900000    11000000    446    0.0186205

chr18    10500000    10600000    chr18    11000000    11100000    413    0.0167251

chr18    10500000    10600000    chr18    11100000    11200000    182    0.00995996

chr18    10500000    10600000    chr18    11200000    11300000    192    0.0109431

chr18    10500000    10600000    chr18    11300000    11400000    147    0.00932337

can anyone help?

many many thanks

TA

Hi-C • 2.0k views

ADD COMMENT • link 5.8 years ago by ta_awwad ▴ 340

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Do the actual contents look like that? Cooler is a binary format (it's hdf5), so you shouldn't be able to see it without a program.