Hello everybody,
I'm trying to perform a Methyl-seq analysis where the aim is to obtain differentially methylated regions (DMRs) between two groups of individuals (mice) grown in different conditions. Nine individuals were sampled on each group and I want to compare their methylation profiles.
I usually perform Methyl-seq analysis using Bismark to map reads and do the methylation extraction and then I usually display those data using Seqmonk. In this particular case I need to find a tool that allows me to perform a DMR analysis with all those samples. I read about MEDIPS, but I don't really understand if this tool cam compare more than one sample for each condition in the study or in the case of having more than one sample for each condition the tutorial states:
"Region informations from several mapping results have to be pooled into one file." (I may be wrong but after reading the MEDIPS tutorial, it seems to me that you have to pool your replicates for each condition to perform the analysis).
Sumarizing, my question is:
Do any of you have any suggestion or knowledge about any software that can accurately perform DMR analysis using as input multiple biological replicates for each condition studied?
Thanks in advance
I'm trying to perform a Methyl-seq analysis where the aim is to obtain differentially methylated regions (DMRs) between two groups of individuals (mice) grown in different conditions. Nine individuals were sampled on each group and I want to compare their methylation profiles.
I usually perform Methyl-seq analysis using Bismark to map reads and do the methylation extraction and then I usually display those data using Seqmonk. In this particular case I need to find a tool that allows me to perform a DMR analysis with all those samples. I read about MEDIPS, but I don't really understand if this tool cam compare more than one sample for each condition in the study or in the case of having more than one sample for each condition the tutorial states:
"Region informations from several mapping results have to be pooled into one file." (I may be wrong but after reading the MEDIPS tutorial, it seems to me that you have to pool your replicates for each condition to perform the analysis).
Sumarizing, my question is:
Do any of you have any suggestion or knowledge about any software that can accurately perform DMR analysis using as input multiple biological replicates for each condition studied?
Thanks in advance
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