methylMnM analysis in non model species?

Rodrigo Jorge Hasbun @Rodrigo_Hasbun3

08 August 2013 2 4K Report

I've started doing studies on methylation using NGS technology in

Eucalyptus globulus. I'm using MRE-seq and MeDIP-seq. So far I have

managed to generate MRE-seq libraries, sequenced by Illumina and mapping

with BWA.

My main problems have been trying to detect

differentially methylated regions. I want to use the package

'methylMnM' but I do not know how to generate it for my species with the files

from the CpG and MRE-CpG site. I have disposed of sequenced and assembled

genomes of Eucalyptus grandis (http://www.phytozome.net/dataUsagePolicy.php?org=Org_Egrandis) and I

would like to know if there is any way to create these files in

order to run 'methylMnM'.

Specifically, my problem is I do not know how to create a bed file with

Mre_CpGsite for my species from the assembled genome Egrandis_201.fa.

I hope you or the community of researchgate can help me.

Best

Rodrigo

Article Comparison of sequencing-based methods to profile DNA methyl...

Viktor Kotolupov

Cancer

http://link.springer.com/article/10.1134/S0022093013020175

Maarten Braspenning

Dear Rodrigo

I work at NXT-Dx, a company specialized in epigenomics and epigenetic testing services. I all of our projects bio-informatics and data-analysis is included. So we are very experienced in analyzing epigenomic datasets and generating lists with differentially methylated regions, etc.

Perhaps we could help you with your project. As mentioned we can run testing services, but we can also simply help you analyze your data or give you some advice on how to do this.

If you can give me some more detailed information I can discuss with our bio-informatics team to see what they could do for you or what tips they could give you.

Kind regards

NXT-Dx

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