search

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
231 stars 70 forks source link

hicPlotMatrix from .hic file issue #687

Closed ptranvan closed 3 years ago

ptranvan commented 3 years ago

Hi

I got a .hic file from Juicer/3d dna and would like to try HiCExplorer for nice heatmap figure, so I did:

hic2cool convert input.hic output

hicPlotMatrix -m output.mcool -o hicPlotMatrix.png 
INFO:numexpr.utils:NumExpr defaulting to 4 threads.
Fontconfig error: Cannot load default config file
INFO:hicmatrix.lib.cool:Could not open cooler file. Maybe the path is wrong or the given node is not available.
INFO:hicmatrix.lib.cool:The following file was tried to open: output.mcool
INFO:hicmatrix.lib.cool:The following nodes are available: ['/resolutions/1000', '/resolutions/10000', '/resolutions/100000', '/resolutions/1000000', '/resolutions/25000', '/resolutions/250000', '/resolutions/2500000', '/resolutions/5000', '/resolutions/50000', '/resolutions/500000']

I am not sure to understand what is the correct way. Thanks for your help.

joachimwolff commented 3 years ago

Please familiar yourself with the data-structure of mcool files: https://cooler.readthedocs.io/en/latest/schema.html#multi-resolution

You need to define the resolution you are interested in because a mcool file contains multiple resolutions. However, this is for a cool file not necessary because it contains only a single resolution. This information is already written in the error message of hicPlotMatrix: Maybe the path is wrong or the given node is not available. and then the possible paths to the resolutions are defined: The following nodes are available: ['/resolutions/1000', '/resolutions/10000',.....]