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bioinfomaticsCSU / deepsignal

Detecting methylation using signal-level features from Nanopore sequencing reads
GNU General Public License v3.0
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How to calculate accuracy and other metrics by evaluate_mods_call.py? #23

Closed vahidAK closed 4 years ago

vahidAK commented 4 years ago

Hi @PengNi ,

I would be very grateful if you could help me on how to calculate accuracy. I know have bisulfite data and methylation_frequency data from DeepSignal. How should I use your script to calculate accuracy? It says I need two result files, one contains calls for methylated sites, another contains calls for unmethylated sites. What is calls for methylated sites (is it methylation frequency file?) and what is calls for unmethylated sites?

Many thanks, Vahid.

PengNi commented 4 years ago

@vahidAK , to calculate accuracy, I choose high-confidence (totally methylated/unmethylated) sites at first. Then I extract modification calls of the standard sites from the call_mods file to two seperate files.

vahidAK commented 4 years ago

Thanks a lot , @PengNi