The methylation information can be imported into SeqMonk whereby '+' reads are methylated and '-' reads are non-methylated cytosines. Use the position value for both start and end of the cytosine methylation calls. You can then perform a probe generation over individual C positions (e.g. read position probe generation) and do a relative quantitation of 'FORWARD' reads 'as percentage of' 'ALL READS'. You could also look at other genomic features such as CGIs, promoters etc.
If you are not necessarily interested in strand specific methylation you can also import *bismark.txt files directly into SeqMonk using the Bismark import filter where you can select the context you are interested in. Hope this helps.
If you are not necessarily interested in strand specific methylation you can also import *bismark.txt files directly into SeqMonk using the Bismark import filter where you can select the context you are interested in. Hope this helps.
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