Unique Mapper

[bshim181]

Hello,

Does Ribotish also only consider uniquely mapped reads similar to lot of other ORF prediction algorithms based on RiboSeq data?
Is there a way to incorporate multimappers? I am trying to see if I could get some riboseq reads mapping to repetitive regions in the genome (TE elements for example).

[zhpn1024]

The default multimapping filters in ribotish are the bam 'NH' tag <= 5 and skipping secondary alignments. If you have additional needs, we can add options to adjust the filter parameters.

[bshim181]

I think it would be helpful if I can have that parameter added in. Thank you so much!

[zhpn1024]

Sorry, the current version has already emplemented these filtering parameters including "--maxNH", "--secondary", "--minMapQ" etc. Try if they can work correctly.