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darelab2014 / Dinopore

DInoPORE: Direct detection of INOsines in native RNA with nanoPORE sequencing
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How can I create my own groundtruth file #6

Closed acarmas1 closed 1 year ago

acarmas1 commented 1 year ago

Hello,

I've been trying to use dinopore from a while. I want to identify A-to-I RNA editing sites from my direct RNA reads.

In the Script #5 one of the parameters is the classref file, which is the groundtruth_class_regression.tsv. However, is this file only meant to be used for the test data set? or should I used it also when running my own data?

If not, how can I generate my own groundtruth_class_regression.tsv file?

itslittman commented 1 year ago

I am also wondering this.

acarmas1 commented 1 year ago

Hello, https://github.com/weir12/DeepEdit I found this alternative to profile A-to-I sites in direct RNA reads. Hopefully, it will help you too.