pb-CpG-tools doesn't emit a methylaton score despite evidence of modified 5mC bases

PacificBiosciences / pb-CpG-tools

Collection of tools for the analysis of CpG data

BSD 3-Clause Clear License

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pb-CpG-tools doesn't emit a methylaton score despite evidence of modified 5mC bases #73

Open indapa opened 2 hours ago

indapa commented 2 hours ago

Hi PacBio team

I have an example where I don;t have a CpG score on a site, despite having evidence of modified 5mC base (colored in red) There is only 8 reads covering the position. Can you help me understand why a score isn't emitted?

indapa commented 2 hours ago

Another question - but this may be an IGV one. Does the blue represent base modification probability less than a certain threshold? Similar to my previous question, cpG tools doesn't emit a score though there is some evidence of a modified base in red.