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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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HiCExplorer with Micro-C data #688

Closed StephenRicher closed 3 years ago

StephenRicher commented 3 years ago

Hi,

Thank you for developing this fantastic tool, I have been using it extensively for my Hi-C analysis. I have some Micro-C data and was wondering if I could use your tool to process this?

Since Micro-C is not restriction fragment based I imagine the key difference between Hi-C will be in the build matrix step. I would like to ignore the restriction sequence based arguments. Is there a way to do this as these argument are now required arguments for hicBuildMatrix.

Thanks very much, Stephen

joachimwolff commented 3 years ago

Hi Stephen,

you can use the older 3.4 version where these arguments were not required. I would be interested to know if that works and if yes, we could discuss ways to integrate Micro-C into the current version.

Best,

Joachim

StephenRicher commented 3 years ago

Hi Joachim,

Thanks for your quick response. Brilliant thanks I will try that and let you know how it goes.

Thanks, Stephen

LeilyR commented 3 years ago

Hi @StephenRicher , would you mind giving us an update about your experince in using hicexplorer on micro-c data?

StephenRicher commented 3 years ago

Hi @LeilyR, sorry I have not had a chance to get back to you on this. I have been a bit side tracked lately, but i still intend to try this and will let you know. If you did want to close the issue I would be happy to just re-raise it as a suggestion later, but I don't mind either way :)

xl5525 commented 3 years ago

I tried my MicroC sample with 3.4.0 without providing enzyme data for QC purposes. And the result seems reasonable.