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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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Error in hicBuildMatrix when multiple restriction enzymes have the same dangling sequence #720

Closed StephenRicher closed 3 years ago

StephenRicher commented 3 years ago

Hi,

I am currently re-processing a published Mouse HiC dataset that uses a 3 enzyme protocol (CviQI, CviAII, and BfaI). CviQI and BfaI have the same dangling sequence (TA) and it looks like this causes an error when using hicBuildMatrix.

The error occurs on line 284 of hicPrepareQCreport.py, when the params dictionary is converted to a pandas dataframe. This raises ValueError: arrays must all be same length as the dangling end TA key now has 2 entries ('dangling end TA': [3665, 0]).

The fact that the second entry has a count of 0 may be inevitable and simply redundant but I am not sure? Perhaps then it would be simple enough just to skip the second entry entirely - this is how I have solved this temporarily.

HiCExplorer (v3.6) Python (v3.8.8)

Thanks, Stephen

joachimwolff commented 3 years ago

Hi Stephen,

thanks for reporting this, I will consider it in the next release of HiCExplorer.

Best,

Joachim