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Additional documentation and examples: EpiNano 1.2

How to train my own SVM model?

In this folder you will find the script train_test.sh, with commands illustrating how to train SVM models and test their accuracies.

How to prepare the input data to train and test my own models?

Please take a look at script run.sh, to see examples on different commands showcasing how to prepare feature tables for training models, as well as making predictions.

Raw data used to train EpiNano 1.2 SVM models

Raw data used to train the SVM models (i.e. m6A-modified and unmodified 'curlcakes') can be found at https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP174366

Reference sequences can be found in cc.fasta

Processed data used to train EpiNano 1.2 SVM models

In this folder, you will also find error and electric signal features extracted with Epinano_Variants and Epinano_Current scripts.

Additional observations regarding EpiNano 1.2 SVM models

  • middleAs means [GCT][GCT]A[GCT][GCT] kmers
  • All A-bases are modified from the mod samples (i.e. curlcakes are modified at 100% stoichiometry).