This is more a question about how STAR works. In figure 1 of the paper (here), the aligner can either look for a splice acceptor site or extend beyond the mismatch. I was wondering how this happens, does STAR try to align the second half of the read, and if that is not possible, will extend beyond the mismatch and try aligning the next part? Or is something entirely different going on?
Thanks,
Matt
Thanks,
Matt
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