Question about long reads splice sites correction

[youyupei]

Hi,

I am reading your paper Transcriptome assembly from long-read RNA-seq alignments with StringTie2. In the section Assemble of long RNA-seq reads, it's mentioned that you correct potentially wrong splice sites by checking all the splice sites present in the alignment of a read with high-error alignment rate. If a splice site is not supported by any low-error alignment reads, you try to find a nearby site.

May I ask how the alignment error rate is defined? And also, it this calculation based on the alignment near the splice site?

Many thanks if anyone could help.