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DMR detection tools for whole genome bisulphite sequencing data in Plants

Hello, I am working on whole genome methylation data in a plant. I am mostly looking for differential CHH and CHG marks. I tried MethylKit. I was looking for some more options on this. Thanks

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updated by Gautier Richard Gautier Richard • written by pixie@bioinfo pixie@bioinfo

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I'm performing WGBS data analysis in plants using the Snakepipes WGBS pipeline. It uses bwa-meth for the mapping, MethylDackel to get the methylation levels and mbias correction and metilene to get the DMRs.

If you have a hard time installing the SnakePipes suite, you can create your own pipeline using these tools. Map the reads with bwa-meth, mark duplicates with sambamba, correct the Mbias with MethylDackel, get the CpG, CHG and CHH methylation levels with Methyldackel using the adequate parameters (--CHH --CHG), perform metilene analysis.

For SnakePipes to run you will need a Slurm queue, follow the SnakePipes installation parameters, modify SlurmEasy a bit for your cluster, createIndices for your reference genome (pipeline provided by SnakePipes). It's worthwhile in long run.

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written by Gautier Richard Gautier Richard

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