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PengNi / ccsmeth

Detecting DNA methylation from PacBio CCS reads
BSD 3-Clause Clear License
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Output reference CGs or not when there are SNVs at corresponding sites of reads #9

Closed PengNi closed 2 years ago

PengNi commented 2 years ago

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If output those CGs or not, when in reference they are CGs, but in reads they are not CGs because of SNV. ccsmeth won't give predictions of those sites, since ccsmeth only predicts CGs in reads.

For now, ccsmeth won't output those sites. Another solution is, as primrose, output those sites as unmethylated (modification freq = 0).

PengNi commented 2 years ago

add option --refsites_all for two ways. See commit 980a14e.