visualize Hi-C .cool file in R
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
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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.
I dump-ed it to txt file by cooler tool