search

novoalab / EpiNano

Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads (Liu*, Begik* et al., Nature Comm 2019)
GNU General Public License v2.0
109 stars 31 forks source link

Apply EpiNano on DNA data? #113

Closed hukai916 closed 2 years ago

hukai916 commented 2 years ago

Hi developers,

Thanks for creating EpiNano!

I have a quick question: is that possible to apply EpiNano-error for DNA modification prediction? BTW, the https://github.com/enovoa/EpiNano/tree/master/test_data/train_models is empty.

Thanks,

--Kai

Huanle commented 2 years ago

Hi @hukai916 , To use it to process DNA data and to rely on the implemented machine learning algorithm, you will have to train models using DNA data. Alternatively, you can use it to generate feature tables and apply simple statistics such as fisher exact test and its likes to detect significant contrasts between samples and infer modifications.

The reposistory has been migrated to https://github.com/novoalab/EpiNano. You will be find models there.