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deeptools / HiCExplorer

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
https://hicexplorer.readthedocs.org
GNU General Public License v3.0
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mapping pipeline #296

Closed mictadlo closed 6 years ago

mictadlo commented 6 years ago

Hi, Do you recommend to use this mapping pipeline ?

Or what is the best practice for mapping?

Thank you in advance,

Michal

bgruening commented 6 years ago

Hi @mictadlo.

Have a look at our tutorial to learn more about mapping. http://galaxyproject.github.io/training-material/topics/epigenetics/tutorials/hicexplorer/tutorial.html#reads-mapping

Cheers, Bjoern

gtrichard commented 6 years ago

In terms of pipelines, I want to drag your attention to the snakepipes: https://github.com/maxplanck-ie/snakepipes

the Hi-C pipeline is based on HiCExplorer and has been developed alongside HiCExplorer at the MPI-IE.