i have the following problem. I am currently comparing the methylation profile around certain genomic regions. I have downloaded methylomes of three different human tissues/cell types from the GEO database. These methylaomes are all in bed format and look like shown below:
track type=wiggle_0 name="UCSD.Spleen.Bisulfite-Seq.STL003:methRatio" visibility=full ..... very long headline
60479 0.730769230769231 .. ..
As we can see, its just a tab separated format. First column = coordinate of methylated C, Second column = methylation ratio of C.
Since i want to compare the methylation profile around a few selected genomic features across my three samples (cell types), I would like to know:
- If a quantile normalization across the samples is necessary.
- If it is necessary, is there a good tool or maybe even an R package, that can be used for this task? Unfortunately, these methylomes are very big (~1.3 GB).
Best regards to everybody :)