jts
commented
1 year ago Hi,
For this purpose it is much better to use the modification caller built into the basecaller (guppy or dorado). It will automatically call methylation at alleles that are expanded.
I hope this helps, Jared
On Tue, Feb 21, 2023 at 9:41 PM NobEura @.***> wrote:
Hello. Thank you for letting us use your great tool.
I have a problem with the methylation analysis of alleles with CGG repeat elongation. In alleles with significant CGG repeat elongation, the number of CpG sites is not being counted. in the BAM file, we have confirmed that the alleles are correctly mapped to the reference with the added repeat elongation.
I would appreciate it if you could help me with a solution.
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NobEura
Hello. Thank you for letting us use your great tool.
I have a problem with the methylation analysis of alleles with CGG repeat elongation. In alleles with significant CGG repeat elongation, the number of CpG sites is not being counted. in the BAM file, we have confirmed that the alleles are correctly mapped to the reference with the added repeat elongation. I would appreciate it if you could help me with a solution.