Hello everyone, I am using Kallisto-Sleuth at the very end of my pipeline in the RNA seq analysis. I'm trying to find on the web (as a newbie) all the reasons in favour of my choice; I would like to ask why choosing Kallisto and Slueth at the end of my pipeline would be a better choice than Deseq2..
Kallisto is not an alternative to deseq2.
Kallisto does the quantification (assigns reads to transcripts). You can run deseq2 on the effective counts output of kallisto (after rounding these counts to integers).
Sleuth is the "alternative" to deseq2.