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In both ssAAV and scAAV, assign the subtype “reverse-packaging” for vector+backbone reads where the vector portion of the alignment overlaps o 5B4C nly the ITR region, not the payload.
To get the ITR region coordinates, consider either of these approaches:
- Take “ITR size” integer input (default 145), and subtract it from the overall "vector" region start and end to get the inner boundary of each ITR -- assumes both ITRs always have the same size.
- Require ITRs annotated in the vector BED with consistent names, similar to the "vector" label requirement.
Ensure this is clear in the written definition and usage docs.
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