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deeptools / pyGenomeTracks

python module to plot beautiful and highly customizable genome browser tracks
GNU General Public License v3.0
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Hi-C matrix format #7

Closed crazyhottommy closed 6 years ago

crazyhottommy commented 6 years ago

I noticed that a .h format is used. I have the raw bin files, how should I change it to the format pyGenomeTracks require?

Bin1    Bin2    Bin3    Bin4    Bin5    Bin6
7.85957 4.80329 11.4766 9.57416 4.5288  8.55022
8.61621 4.98956 2.35654 5.69483 11.1187 10.1322
4.06803 4.07801 7.98047 2.59144 6.3851  7.74306
4.52869 2.70624 8.94544 4.29185 8.29491 8.38257
2.91472 3.84658 1.56752 4.48515 7.4955  8.77461
3.08096 2.96487 7.23623 2.33142 3.08529 5.5379
3.12141 3.06905 4.97247 2.39298 5.03621 7.22344
3.4037  2.26455 1.48176 1.41958 3.40252 7.7027
3.8696  1.41425 7.68872 2.21027 5.06846 3.20063

Thanks, Tommy

fidelram commented 6 years ago

take a look at http://hicexplorer.readthedocs.io/en/documentation/content/tools/hicExport.html

That will take a matrix in different formats and export them as a hicexplorer format (.h5)

I think the ren format may be the one you need. The documentation has some explanation of the format (in the readthedocs page you will need to scroll to horizontally to read the full explanation).

crazyhottommy commented 6 years ago

Thank you very much for the link!