Question: How do I find out regions of methylation enrichment using MEDIPS bioconductor package?
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gravatar for Vijay Lakhujani
2.5 years ago by
Vijay Lakhujani4.0k
India
Vijay Lakhujani4.0k wrote:

I have a single MEDIP-seq sample and I am only interested in finding out regions of methylation. How do I go about it? Since, I am not interested in differentially methylated regions (DMR's) as I don't have multiple samples, how could I achieve the same using MEDIPS?

Why MEDIPS?

I know there are a lot of tools available but this one is highly cited and used. There are other tools which in turn use MEDIPS at the backend (example - MeQA).

What has been already done?

Since I am working with a genome which is not already present in the MEDIPS custom genome package (BSgenome), I was able to create one for myself based on below guidelines and forge it into BSgenome.

Here is the Forging_custom_genome_tutorial

Now, I am looking at this tutorial.

The problem:

The methodology has been beautifully explained for the demo dataset called "MeDIPSdata" provided within MEDIPS package (which consists of a couple of BAM files),however, it is not clear to me as to how to proceed with a single BAM file (since I have a single sample)?

  1. Which steps are important and cannot be skipped (QC, normalization)?
  2. How to find regions of methylation for a single sample?

PS: Respond only if you can help me with regards to MEDIPS package. No other package information would be useful for me.

Thanks

methylation medips medip-seq • 801 views
ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by Vijay Lakhujani4.0k
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