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Does pileup always output a value for a covered base? #200
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Hello @Ge0rges, Any position with valid coverage >0 will have a bedMethyl record.
I would say "For any given location/nucleotide, if there is no methylation but there is coverage of that base and the modification call passes the confidence threshold, will N canonical always be non-zero?" Let me know if you find this to not be the case. |
So just to double check, even if a base is not methylated but covered it could not show up if the modification call isn't above the threshold? Would it be incorrect to treat covered bases below the threshold as unmethylated? I guess unknown is different that unmethylated... |
A potential confusion is that For example (take a simple 5mC/canonical example): However if the threshold is If a read is filtered out, it adds a count to column 16 not You can, however, force a default to canonical call by setting the thresholds specifically for each modified base |
Hi,
Just a simple question (for once), I wanted to ensure I understand the output of pileup correctly. For any given location/nucleotide, if there is no methylation but there is coverage of that base, will
N canonical
always be non-zero?The text was updated successfully, but these errors were encountered: