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Using a MTAse Ko mutant instead of WGA #76
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Hello @kafker, Yes, this is a perfectly good solution for identifying exact matches between methylation motifs and their Mtases. By running I'll be interested in hearing back from you if you pursue this type of experiment as we made only few of this type of experiment. Best, Alan |
Hi Alan, I will keep you updated Best |
Hi Alan, Just a quick update. I am struggling quite a bit with
The computing node that I am currently using has 2 x CPU with 24 cores each, 2.4 GHz, and 384GB RAM. In trying to run nanodisco difference on a fill genome (1835 chunks) and in two days I got only 460 chunks. Probably I will need to relaunch the analysis on a node without a In the meanwhile, I used deepmod2 on the WT and KO mutant and, as expected, I am observing huge differences in the read methylation fraction at the level of Mtase methylation motifs. Since we do not have a WGA, I think It would make more sense to subset of the reference genome to specifically targeted the regions of interest. I will keep you updated and thank you for your support! |
I used nanodisco for WT and MTase mutant, it worked well. |
Dear devs,
I understand that nanodisco requires a WGA sample. However, I was wondering if a KO mutant for the methylase of interest (we already know the methylation motif) could be a "good" substitute for the WGA sample.
In theory, differences between the current of WT vs the current of the KO mutant strain should be observed only at the level of the methylation sites.
Perhaps I am missing something so I would like to hear your opinion.
Thank you!
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