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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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when I want to use hicFindEnrichedContacts to find the enrich interaction ,I can't fiand which parameter for input? #327

Closed hzaumsq closed 5 years ago

hzaumsq commented 5 years ago

hicFindEnrichedContacts --outFileName OUTFILENAME --method {z-score,obs/exp} [--perchr] [--skipDiagonal] [--depth DEPTH] [--help] [--version] can you give me an example to show use this function?

gtrichard commented 5 years ago

Dear @hzaumsq , thanks for using HiCExplorer.

hicFindEnrichedContacts can be used to convert a matrix to z-score or obs/exp matrix using the following:

hicFindEnrichedContacts --matrix data.h5 --outFileName data_z-score.h5 --method z-score --maxDepth 20000000

will output a z-score matrix with bins separated at most by 20 million nucleotides.

hzaumsq commented 5 years ago

The same error as follow： hicFindEnrichedContacts --matrix egg_vs_J2_10k.h5 --outFileName enrich.h5 --method z-score --depth 20000000 usage: hicFindEnrichedContacts --outFileName OUTFILENAME --method {z-score,obs/exp} [--perchr] [--skipDiagonal] [--depth DEPTH] [--help] [--version] hicFindEnrichedContacts: error: unrecognized arguments: --matrix egg_vs_J2_10k.h5

gtrichard commented 5 years ago

Are you on the master branch? I tried with the release22beta branch and it was working. With this branch executing hicFindEnrichedContacts gives:

usage: hicFindEnrichedContacts --matrix MATRIX --outFileName OUTFILENAME
                               --method {z-score,obs/exp} [--perchr]
                               [--skipDiagonal] [--maxDepth MAXDEPTH] [--help]
                               [--version]

Where --matrix is required.

You can conda install hicexplorer==2.2beta