Entering edit mode
2.2 years ago
whiteerosee8
•
0
Hello all,
I have whole genome bisulfite sequencing for two cell populations. One of my cell populations has "pure" cells (Pop1), while my second cell population has a mixture of two cells (Pop2) including cells from my first population. Is there a way to subtract the dna methylation sequences of my Pop1 from my Pop2? That way I can perform methylation calling after subtracting the populations.
Thanks for your help!
What you are asking for sounds impossible to me. You couldn't know if methylated loci found in the second sample were shared among cells or from Pop1.
In downstream analyses you could identify loci that are putatively only found in Pop2. But since you have pooled populations in the second sample there is also no guarantee these methylations are not also found in Pop1, and not present in the first sample and due to sample heterogeneity. Sampling replicates would help alleviate this issue.