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dpryan79 / MethylDackel

A (mostly) universal methylation extractor for BS-seq experiments.

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Counts reported for G positions

dataMaster-Kris opened this issue · comments

commented

Hi,
In the bedgraph output, I was expecting only the C postions in CpG sites. However, when my reads map to both the OT and OB strands, methyldackel reports methylated counts for both the C and G positions in CpG sites. Is this expected? How do I interpret the counts for the G positions?

commented

Ok, I got it. When read maps to the bottom strand, the G position on the OT is actually C for the OB.