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cerebis / qc3C

Reference-free quality assessment for Hi-C sequencing data
GNU Affero General Public License v3.0
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Support for Arima High coverage Hi-C kit #61

Open Norbittner opened 2 years ago

Norbittner commented 2 years ago

Hi,

for a new version of qc3C it would be nice to support the 4-emzyme cocktail of the Arima High coverage Hi-C kit. At the moment only max. 2 enzymes are supported.

cerebis commented 2 years ago

Thanks for bringing this to my attention.

In truth, some parts of the qc3C codebase can handle an arbitrary number of enzymes, but there are also a few methods where I chose to make the interface simpler/explicit. I will have to see how much refactoring is required, to have an idea of when this could be accomplished.

Also @Norbittner, it would be really helpful if you could assist me by providing an accession to an example of this datatype.

Norbittner commented 2 years ago

Hi @cerebis
Thanks for the fast reply. I will have a look for any public datasets (i use clinical data atm which are not open) but it might be hard as the new Arima kit is quite new. But i'll let you know.

AlcaArctica commented 11 months ago

Has there been an update on this? Our lab has also used a combination of 4 enzymes (DpnII, HinfI, DdeI, MseI) from this kit https://arimagenomics.com/wp-content/files/Bioinformatics-User-Guide-Arima-HiC-and-Arima-High-Coverage-HiC.pdf and I am not sure how to analyse the resulting data.

ferrojm commented 8 months ago

Hi @AlcaArctica! Did you have good results by using these enzymes as input for qc3c for Arima High coverage kit?

AlcaArctica commented 8 months ago

@ferrojm Sorry, I have not tried this so far. Have you?

ferrojm commented 7 months ago

@AlcaArctica No :( I think I will try a mapping approach!

Rhia15 commented 4 days ago

Hey, my lab is also using the new Arima kit, just wondering how you guys analysed how effective the HiC library were? Did you still go ahead with qc3c?