Hi I have a very basic question regarding the analysis of whole genome methylation sequencing data. I have read some papers they have used MACS peak caller for doing data analysis. I know this software is frequently used in ChIP-seq analysis but for methylation analysis also can we use it. I see HOMER has a module to do so. By looking in literature I see people use different softwares like Bismark, or MEDIPS generally for such data. So will it be wrong to use MACS for analysis?
I have one more question regarding pooling of normal samples BAM files is it good to make a merged file and use it as a background for all the samples or not? What are the merits or demerits of doing so?
I will thankful if can get some input as I am bit confused to what is the right strategy to follow.