Different coverages for different --np_tresholds for ONT data.

[ljcousse]

For a project analysing ONT data, we wanted to check the impact of using different cut-offs ("--np_tresh") in the bam2pat function. I.e. we expect that for a more stringent cut-off less CpGs to be called as methylated. However, after loading the beta files into R (using the code from the docs), we also find differences in coverages between different cut-offs although the number of covered CpGs should be the same?

E.g.: with "head(content_25)", the first 6 CpGs using a --np_tresh 0.25 and "head(content_75)", the first 6 CpGs using a --np_tresh 0.75

print(head(content_25))
[,1] [,2]
[1,] 5 5
[2,] 5 5
[3,] 3 3
[4,] 6 6
[5,] 5 5
[6,] 5 5
print(head(content_75))
[,1] [,2]
[1,] 4 4
[2,] 2 2
[3,] 3 3
[4,] 6 6
[5,] 5 5
[6,] 5 5