Kallisto handling multiple reads from single transcript?

[stromk]

Hello!

Is it possible to tell Kallisto that two or more reads originate from the same transcript? I don't want these to be double counted.

Thanks!

[Yenaled]

kallisto is an RNAseq quantification algorithm that assesses gene expression -- if you have two reads originating from the same transcript, that transcript will get two counts. That's how gene expression quantification is done and is the main purpose of kallisto.