I have run some genome-wide comparison of methylomes from two biological replicates. The results are showing there are many Differentially Methylated Regions (DMRs) between these two samples. I wonder if anyone has experiences in sequencing data analysis?
If there are many differences in the sequencing data between two biological replicates, what could be the potential explanations? Here is more detailed information on these two samples: (1) they are both from male rats; (2) they are from two generations (one sample is from the F1 generation, the other sample is from the F2 generation). (3) They are genetically identical.
So, although I call them 'biological replicates', they are not really 'biological replicates', it is only that they are genetically identical. I think there can be several factors that cause the large number of DMRs between these two samples:
1) Batch effects? (The sequencing libraries of these two samples were generated in two different batches).
2) Generation effects? (I am not actually sure what kind of factors can be included here)
Or any other factors that you guys can help me think of?
Do you think there are ways to really tell what is the most likely reason for these DMRs?
-Jackie
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