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Calling 5hmC

2

Hi! I'm interested in calling 5hmC throughout CpGs across the genome, and I wanted to clarify how best to do that. At this stage, I'd like to focus solely on...

KevDonn

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...

OceaneMion

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...

OceaneMion

DMR without pileup

4

Hey, I have (summary) BED files and I wanted to know if I necessarily need the bed file from pileup to run dmr. The samples I have is not compatible...

ArnavBharti

how to allele-specific methylation calling?

1

Hi, may i inquire how to do allele specific/happlotype resolved methylation calling and analysis? a look in the literature requires phasing tools like whatsapp etc... i already did base calling...

sahuno

Convert bam to pseudo bisulfite output

37

Is there a way to convert a modified mapped or unmapped bam containing the MM/ML tags into a pseudo bisulfite output? In other words, convert every unmodified C to T...

faulk-lab

num-reads not working

3

Hello! I have memory of 197G and it's not enough for summary of whole bam and even while trying to work with chromosomes there is the same problem with summary...

ShokodkoMariia

modkit dmr - failed to read tabix index

6

Hello ``` mod_kit 0.2.8 ``` I am getting a very basic error: ``` > Error! failed to read tabix index "barcode05_E_CHH.bedmethyl.gz.tbi" > caused by invalid reference sequence names > caused...

lilypeck

Validation with ground truth

2

Hi, I have a few questions regarding the use of modkit validate. 1) Can you please demonstrate an example of a ground truth bed file required for modkit validate? If...

vyx-lucy-kaplun

How to detect the background noise from control and test samples

2

Dear developers, Attached are the results for two samples: 1# (control) and 2# (modified_test), generated from the modkit summary and modkit sample-probs using default parameters. I am uncertain about how...

xiangpingyu