Hello, sorry for this question, but how is supplementary alignment determined (the algorithm)? I know it is chimeric reads, but I was really surprised to have 60% of chimeric reads in my samples after MDA 🤔
Also, I checked some publicly available datasets and was surprised to see that even without MDA there are 4.5-12% reads having SA flag (PacBio, ONT). Isn't it too much structural variation to expect.. ?
Hello, sorry for this question, but how is supplementary alignment determined (the algorithm)? I know it is chimeric reads, but I was really surprised to have 60% of chimeric reads in my samples after MDA 🤔 Also, I checked some publicly available datasets and was surprised to see that even without MDA there are 4.5-12% reads having SA flag (PacBio, ONT). Isn't it too much structural variation to expect.. ?