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!

[ericmalekos]

I am also interested to hear how multimapping reads are treated by Ribocode

[FeliciaJiangBio]

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!

Hi! I confronted the error of "not unique alignment" when doing ORF counting. I think this error may induced by the outFilterMultimapNmax parameter setting in STAR alignment. Could you please provide the site of the documentation you mentioned related to recommendation of outFilterMultimapNmax 1 ?