1) How to calculate the coverage of CpG sites of the MeDIP & MRE data? (can anyone give me some details on this)?
2) How to do saturation analysis? I know what saturation analysis mean and I know the purpose of doing it. I just have no idea how the analysis should be performed. I was asked to write an R or Perl script to do it. Can anyone give me some information on the algorithm or direct me any useful online sources?
Thank you very much!
please ask "NXT-DX", a small company in Blegium specialised on MBD-NGS, or Christoph Bock at the CeMM in Vienna
We've been using MEDIPs (an R based package that's part of bioconductor), there's a decent tutorial for it (attached). The only issue we had is that we're working with pig, so we had to do some things to format the genome in a way MEDIPs accepted. The package has various analyses you can do, including saturation analysis, CpG enrichment and identifying DMRs. I'm guessing that this might be a good place for you to start.
There is also MeQA (described in Huang et al., 2012 on Bioinformatics). I'm just reading the paper and the documentation, and I don't know if it would actuallywork for your purposes.
I can only suggest you to read the paper and browse their website (http://life.tongji.edu.cn/meqa/). It should work fine, and it should be also easy-to-use.
Basically, it is a complete pipeline to assess data quality in MeDIP-Seq experiments and to detect differential methylation among samples. It employs other open-source tools (i.e. SAM tools, MEDIPs), and is written in shell script, Python and R.
I hope it may help you.
Gina I'm working with a non-model tree species (Eucalyptus globulus). I need to do data methylation analysis from MRE-seq experiment but I don't have Bsgenome for apply MEDIPs pipeline. Can you give me the indication to format my genome for ME DIPs? I try to use forge instruction but my experience in bioinformatic is not sufficient. Your experience with pig is very important for me.
http://www.bioconductor.org/packages/2.12/bioc/vignettes/BSgenome/inst/doc/BSgenomeForge.pdf
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