I would like try HISAT2 for aligning RNA-Seq data but I am uncertain about using the -k parameter for reporting N multiple alignments. The manual says a primary alignment is an alignment whose alignment score is equal or higher than any other alignments. But it also says HISAT2 does not guarantee that the N alignments reported are the best possible in terms of alignment score. Does this mean i) the N reported alignments may not be all alignments with the best alignment score or does it mean ii) there may be alignments with a better score than of those N reported?
i) would be clear, but in case of ii) I don't understand how this is possible if a primary alignment has an alignment score equal or higher than any other alignments.
Thanks in advance!