Generate Simulated data for Differentially methylated regions (DMRs)

Hi all

I want to generate simulated data to test the algorithm for finding deferentially methylated regions (DMRs) of a WGBS data between case and control. Could anyone help me with the process of doing that.

next-gen-sequencing

• 2,667 views • link

updated 3.5 years ago by Ram

• written 11.3 years ago by anonymous •

1 answer

Have you tried Google?

There was a recent Bioinformatics paper describing exactly this.

• 0 views • link

updated 3.5 years ago by Ram

• written 11.3 years ago by mark.ziemann

More posts like this

Homer annotatePeaks for enrichment analysis
written 3.4 years ago by Joana •

I want to test differentially methylated regions (DMRs; identified in whole genome bisulfite sequencing data) for enrichment of certain genomic features. For example, do I …
Downloading WGBS sequencing reads for cancer sample and healthy sample
written 5.0 years ago by Nishat •

Hello, I am completely new in WGBS data analysis. I want to learn analysing differentially methylated regions between cancer and normal sample. How can I …
How to calculate foldchange for log2'd expression data?
written 5.9 years ago by SupBioInformatics •

Hi, I have a math question. I am doing differential expression test. My expression data is already log2'd. I would like to perform t-test between …
How to test differential methylated regions in R
written 6.7 years ago by Shaway •

Hello, I'm doing some research in WGBS and want to distinguish differential methylated CpG island from tumor and normal (10 samples for each group). I …
Is there any software to generate simulated WGBS data based on a background
written 7.4 years ago by Shaway •

Hi everyone, I want to generate some simulated data based on cancer(case) and normal(control) people's WGBS data, then I can evaluate some algorithms by changing …
From WGBS-seq to DMR calling and annotation
written 8.2 years ago by zhengyunchaosky •

Hi, friends, I am new in Whole Genome Bisulfite Sequencing (WGBS-seq) analysis. About Differentially Methylated Regions (DMRs) calling, I have read some papers directly using …
annotation of RRBS DMRs in RnBeads or other packages
written 8.6 years ago by rahel14350 •

I used the mean methylation value and Wilcox test to define differentially methylated regions between two groups of RRBS data. Is there any way that …
Length of differentially methylated regions
written 9.2 years ago by niutster

Hi, I want to identify significant differentially methylated regions from a set of DMRs which has DMRs with length from 1 bp to 200 bp, …
minfi package, DMRs,
written 9.8 years ago by niutster

Hi all, I have a idat file contains three types of experiment: control, patient and suspected people, i want to find DMRs between patient and …
Differentially Methylated Regions finding in time series experiment
written 10.5 years ago by antgomo •

Hi, I am dealing with Whole Genome Bisulfite Data (WGBS), form a time series experiment (4 stages), and I am wondering I f I could …