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Just now, a idea emerged in my mind. I'm planing to align reads from ChIPseq to Mus musculus (C57BL/6J mouse reference genome) in which all SNP positions are masked by the ambiguity base ’N'. And then, the SNPsplit can be applied to assign reads to paternal or maternal genome. Since the parental strain of hybrid mouse are C57BL and PWK strains and the SNPs in vcf file are relative to the C57BL/6J mouse reference genome, I don't know whether this method can work out. Can you give me some suggestion?
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