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3DGenomes / TADbit

TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models
GNU General Public License v3.0
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Incompatible cooler format #358

Closed vntasis closed 3 years ago

vntasis commented 3 years ago

Hi. I am using tadbit tools. I have tried to export the results of an analysis to a cooler file with both tadbit bin and tadbit export. However, when I try to inspect the file with either the cooler library or with the HiCExplorer's hicInfo utility, I get an error of the type: " Exception: Matrix failed to load: 'No cooler found at: output.cool.' ". Is there something wrong with the cooler output or am I missing something?

Thanks a lot.

david-castillo commented 3 years ago

Hi,

We generate a multi-resolution cooler file. If you have exported the matrix at 25000 with cooler you can inspect the file with cooler info output.coolcooler.mcool::resolutions/25000 You have to append "::resolutions/" to operate with the cooler.

Can you try that?

David

vntasis commented 3 years ago

Thanks for the quick response. Now I see that it is a mcool file. It worked by appending "::resolutions/" at the end, i.e. cooler info output.cool::resolutions/10000.

Vasilis