Hello, Elizabeth,
Recently , I test the scripts on my AAV data. I'm little confused with the output result - "aav.summary.csv".

1.about results header annotation
The "map_subtype" column defined reads types. And it looks like that "3-partial" describes the reads containing left ITR but no right ITR, and "5-partial" goes opposite way, right? Do you have any detail description files of "column name".

2. about 3-partial definition
In my AAV vector, the AAV region with ITR is "700-5800". I filtered out "3-partial" reads, and find that some “600-700” reads are also defined as "3-partial". But "5-partial" filtered results contain those reads exactly within the range "750-5800". As my understanding, the “600-700” reads may belong to "backbone|3'partial" . Am I missing some parameter setting when runing "summarize_AAV_alignment.py" scripts?
command：python summarize_AAV_alignment.py AAV.map.sort_by_read.sam annotation.txt AAV --cpus 24

Thanks,
Guliba.