kallisto quant allow for multi-mapping

[cmswan23]

Is it possible to include reads pseudo-aligned to multiple genes using kallisto quant for bulk RNAseq data? I have an index of only multi-copy genes and do not want to discard data due to multi-"mapping".

[Yenaled]

I don’t understand the question. Kallisto (by virtue of it being an pseudoalignment algorithm) always retains multimapping information and uses it to generate the estimated counts in the abundance output file.