OceaneMion

Obtain Global methylation level of the genome

9

Hi all, I would like to know how can we obtain the global methylation % of a genome using modkit pileup. I know that with the fraction modified I Can...

What is exactly mod_qual?

3

Hi I would like to know the difference between mod_qual and fraction modified ? What do you mean exactly by mod_qual, I know that fraction modified is basically the number...

Perform DMR analysis on the same file

3

Hi again all, I would like to know if it is possible to perform a DMR analysis on the same file (I want to compare contigs methylation from the same...

Perform mean of probability for each read position with modkit extract

15

Hi all, I would like to know if it is possible to write some bash code after performing a modkit extract, to filter based on ref_position and chrom. For example...

Are all CpG reported ?

7

Hi I would like to know if all CpG are reported in the modkit pileup if we specify no-filtering ? Even those that are not methylated ?

More precision on how are base modification probabilities calculated with Modkit

4

Hi, I have read the documentation on base modification probability calculation, but some points are still not completely clear to me. I would really appreciate it if you could help...

Calculate methylation coverage genome wide

1

Hi, I am currently working with Modkit and would like to know if there is a way to extract the global CpG methylation coverage (I am focusing on 5mC) from...

Hi, I would like to know if you have a function to plot mapping coverage along the chromosomes, I saw it in your youtube video of: Visualising Nanopore Methylation Data...