Question about calculation of base counts in hisat3Ntable

[shen-lanlan]

Dear developer,

Recently I have been using HISAT-3N for my analysis and this is really a great software. But I have a few questions regarding how the base counts are calculated in hisat3Ntable and whether there are any specific cutoffs set for this calculation.

Because I noticed that when using bam-readcount in the same unique mapping mode, the base counts obtained seem to be slightly higher compared to those obtained from hisat3Ntable. Could you please provide some insight into the algorithm or approach used for this calculation? It would be helpful to know the details to better interpret the results.

Thank you for your time and assistance. I appreciate any information or clarification you can provide regarding these questions.