In both ssAAV and scAAV, assign the subtype “reverse-packaging” for vector+backbone reads where the vector portion of the alignment overlaps only 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.
In both ssAAV and scAAV, assign the subtype “reverse-packaging” for vector+backbone reads where the vector portion of the alignment overlaps only the ITR region, not the payload.
To get the ITR region coordinates, consider either of these approaches:
Ensure this is clear in the written definition and usage docs.