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GoekeLab / xpore

Identification of differential RNA modifications from nanopore direct RNA sequencing
https://xpore.readthedocs.io/
MIT License
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run without KO sample #147

Open xieyy46 opened 2 years ago

xieyy46 commented 2 years ago

Hi Xpore team! I' d like to know if it is possible to run Xpore without a control sample (like KO sample), and this is the case where I only want to get the modification rate of a site in a sample? As Xpore models a mixture of two distributions corresponding to unmodified and modified reads in a given site, in principal, Xpore can finish this without control sample.

yuukiiwa commented 2 years ago

Hi @xieyy46,

To detect m6A without a control sample, we would recommend using m6anet from our lab, which outputs a probability of whether a site is m6A. Here is the page to m6anet: https://github.com/GoekeLab/m6anet

Thanks!

Best wishes, Yuk Kei