"C strand" and "G strand" from bisulfite converted bam files
We know to calculate methylation value for a CpG position from the bam file we have to consider "C strand" and "G strand". I am a little confused about how to determine which read is "C strand" and which is "G strand" from the bam file? It seems a typical bisulfite aligner adds a tag to the bam file about the Bisulfite conversion strand label (like the YD tag here). I guess I have to use this tag but not sure how.
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