Hi, This question is to the people who have worked with RRBS methylation data and RNASeq data. I have RRBS methylation data for cell lines and the RNASeq data for the same cell lines. For RNASeq data I have used cuffdiff program for differential expression analysis but I am not quiet happy with it as it does not give per sample fpkm or read count information so that I can compare the expression in groups with the expression of each sample in those groups to validate the results of differential expression analysis. I would like to use other method of differential expression but I have a question that since I will be integrating the data with RRBS, should I consider only the method which generates the read counts in fpkm units(like cufflinks-cuffdiff)? I am thinking this because fpkm normalizes the reads by transcript length which other methods do not.

My second question is that is there a standard method to integrate RRBS methylation data and RNASeq paired end data?

Any suggestions will be greatly appreciated. Thanks.