Using Modkit pileup --modified base C

[serignebasse]

Can someone explain me How Modkit compute Nmod (for 5mC). They do it per reads all they use all reads aligned on same position and count number of read with modified C.

• Nmod - Number of calls passing filters that were classified as a residue with a specified base modification.

[ArtRand]

Hello @serignebasse,

I apologize for the slow response. Basically, each read aligned to a cytosine (or a CpG dinucleotide, depending on your settings) with a C-base modification call will be evaluated. If the probability of the call (modified or canonical) falls below the filter threshold it is counted in N_fail, otherwise it's called in N_mod or N_canonical depending on the call. There is more detailed documentation here.