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Default parameters used in Event detection function
Hi there,
I have some questions about the event detection, which I knew was adopted from nanopolish/scrappie. I found the default parameters were different between RNA and DNA event detection.
static detector_param const event_detection_defaults = {.window_length1 = 3,
.window_length2 = 6,
.threshold1 = 1.4f,
.threshold2 = 9.0f,
.peak_height = 0.2f};
static detector_param const event_detection_rna = {.window_length1 = 7,
.window_length2 = 14,
.threshold1 = 2.5f,
.threshold2 = 9.0f,
.peak_height = 1.0f};
I could quite understand the reasons: 1. RNA molecules translocate much slower than the DNA (larger window length), 2. RNA signals were more fluctuation (higher threshold and peak_height). Correct me if I were wrong.
I think the settings were quite reasonable. I raised the issue here just to ask for a feature in the "f5c eventalign" function, which I could specify these default parameters. I knew I could fork the repo and modify the default numbers and then compile to binary f5c to do the test, but I think exposing these numbers to the command line args will help me a lot, reducing manual works.
Best, Logan