OceaneMion

Yes thank you but the value obtain in modkit pileup for the methylation is really different, is it because it is averaging the methylation of each reads at each genomic...

> modkit pileup $modbam $pileup_bed --combine-strands --cpg --only-tabs [--ignore h] Hi I do not want to apply any threshold the goal is to have all the potential methylated sites, so...

Thanks for your awnser, Do you think it is possible to obtain the values from modkit dmr using only one bed file and a reference genome, to have the information...

Thank you for your awnser, yes I think pileup is more suitable indeed. But I don't exactly understand how pileup works ? This is an example of the first lines...

I may have another question, is the bedgraph 4th column giving me the probability of the methylation at a specific position it look like this : contig_1 2 3 0.8321168...

Thanks a lot ! So if I want to plot the probability distribution of each modified bases at each genomic position, I will need to use the fraction_modified values right...

Thanks a lot ! I think it is Indeed better to keep only the cpg with coverage. What I would like to know also is how to get a table...

Thanks for your awnser yes if I do not put a threshold therefore I will have the same number of 5hmC and 5mC here, which is then more accurate to...

Thanks a lot, it is much clearer to me now, but I was wondering about cases where I have a very low Nvalid_coverage. For example, in my samples I have...

It seem that when I specified the cpg tag my coverage is a lot better, is it because modkit try to predict other site then CG without the cpg tag...