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.
I think it is helpful to have more than one pipeline in mind because, as I have run into, sometimes a tool just will not work. I can't open the kallisto created h5 files with sleuth because of the environment in which they are created and have yet to figure out how to change it so it will work. Note: NOT asking that as a question here, simply saying that with these tools it is also a good idea to know your options because sometimes they don't work and you need results by X day without necessarily the time to fix the issue.