Question on handling multimappers

[mosi223]

Dear RiboCode developers,

According to the documentation, it is recommended to include outFilterMultimapNmax 1 parameter in STAR alignment to exclude non-unique alignments and reduce noise for downstream analyses.

In case of default outFilterMultimapNmax 10 setting, how does RiboCode handle non-unique alignments? Are they included in P-site estimating and ORF detection? Does RiboCode differentiate between primary and secondary alignment flags when dealing with multi-mapped reads?

Thank you very much!