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  • HISAT-3N: Finding Methylation Context

    I am a new user of HISAT-3N and am using it to analyze samples from a modified BS-seq experiment. I have generated the HISAT-3N conversion table which includes converted and unconverted counts by position. Is it possible to determine the context as I would like to differentiate CG, CHG or CHH? (I see one can specify CG only.) I note that other BS-seq packages like Bismarck provide this context.​ As I have built a pipeline using HISAT-3N, I would rather not start over with a different tool.

    Thanks in advance for you any help or advice.

    Best,

    Bryan

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