-
By looking at the coverage analysis, you mentioned the methylation-effective several times, but could you be more specific about this definition. What is "methylation-effective"? A formula would be fi…
-
Hi there,
I would like to apply OFF-PEAK to some targeted EM-seq data (obtained using the Twist Methylome Panel). However, since the tool was designed specifically for exome sequencing data, all ta…
-
**Version info**
- bcbio version 1.2.9:
- OS Ubuntu LTS 20.04:
**To Reproduce**
Exact bcbio command you have used:
```
bcbio_nextgen.py ../config/CTRL-MDD-S-MDD.yaml -n 72
```
Your yaml …
-
I have been toying around with how to make tracks that show methylation in CpG, CHG, and CHH sequence contexts. The annoj browser does it very well (http://neomorph.salk.edu/epigenome/epigenome.html),…
-
Hello,
I have methylation data from the EPIC V2 array and I wish to deconvolve it (to the different PBMC cell types). My problem is that all the packages I found that deal with deconvolution of met…
-
Hi anders,
Very powerful and effective tools for single cell methylation data analysis, but I wonder if you have consider the batch efforts across different library, and how to remove batch effort …
-
Hello Alex,
I have a small question about RRBS methylation data.
It is my question that I post before.
My question this time is how to use RRBS methylation data to do a boxplot based on CpG s…
-
Dear
I'm trying to generate a matrix in order to make metaprofile . the input data are methylation in bigwig format. The problem is that in my matrix a lot of values are indicated as nan and othe…
-
ONT is now making methylation analysis a bit easier, in some cases it can come for "free" now with base calling. Their new base caller `dorado` https://github.com/nanoporetech/dorado can now generate…
-
Hi!
I've just been your new paper on epigenetic predictors of maximum lifespan (It's great stuff!)
In the paper you say:
"Specifically, we calculated the mean methylation value for each CpG wit…