IPD values from ipdsummary, methylation analysis using PacBio
Is there anybody familiar with methylation analysis using PacBio data?
I ran the ipdsummary tool from smrtlink package. The minimum coverage and p-value were set to 50X and 0.001, respectively. The methylation rate is about 2% of the total bases with IPD values ranging from 1 to 13, and QVs ranging from 2 up to 300.
The question is, should I apply additional filters to visualize the results? IPD values around 1-2 are confident values? Should I use the QVs for additional filtering?
I have read the white paper but it is not very clear about this.
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