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XiaoTaoWang / EagleC

A deep-learning framework for predicting a full range of structural variations from bulk and single-cell contact maps
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Hi-C 3.0 with DdeI+DpnII #34

Open gibcus opened 10 months ago

gibcus commented 10 months ago

Xiaotao, This looks like an amazing tool and I would love to give a shot on our newer Hi-C protocol that uses DdeI and DpnII. I know your code can work with Arima, so is there something you or I can do to make this work for Hi-C with DdeI and DpnII dual digestion?

Johan

XiaoTaoWang commented 10 months ago

Hi Johan,

Since the contact patterns used by EagleC for SV detection are not likely to be affected by the enzymes used in Hi-C, I believe the current models can be directly applied to detect SVs on your matrix. Please give it a try and let me know if you have any problems in running the program :)

Xiaotao

gibcus commented 10 months ago

It seems to work if I use ICE! However, if I want to use CNV, I'd have to use neoloop finder and specify an enzyme, right? Using neoloop finder would be great, because to do a good compartment analysis on some of my coolers, I would need to remove the CNV bias.

XiaoTaoWang commented 10 months ago

I see. Yes, you need to run NeoLoopFinder to perform CNV normalization. I will update it soon to make it work for "DdeI+DpnII" and keep you informed.

Xiaotao

gibcus commented 9 months ago

Hi Xiaotao, I'm folllwing up on the above. Please let me know if it would work if I adapt calculate-cnv by adding Dde-DpnII to this line:

parser.add_argument('-e', '--enzyme', default='MboI', choices = ['HindIII', 'MboI', 'DpnII', 'Arima', 'BglII', 'uniform'],
                        help='''The restriction enzyme name used in the Hi-C experiment. If the genome
                        was cutted using a sequence-independent/uniform-cutting enzyme, please consider
                        setting this parameter to "uniform".''')

And provide a weblink with 'hg38.DpnII-DdeI.npz'

XiaoTaoWang commented 9 months ago

Hi Johan,

Sorry for the delay. You were right; that's all we need to make it work for Dde-DpnII. I have generated the npz file, which you can download from the link https://www.jianguoyun.com/p/DS6GgfsQpPuuDBjNlsIFIAA. However, I haven't had the time to test it. Please feel free to download the file and modify the script as needed.

Xiaotao