Hi, you can use tximport, then SARTools to do such analysis. Please note, that the next DESeq2 update will include tximport as a function.

Thibault

I have not tested, but it seems that what you are looking for is explained here (at least, for human data):

https://rawgit.com/pachterlab/sleuth/master/inst/doc/intro.html

At this point the sleuth object constructed from the kallisto runs has information about the data, the experimental design, the kallisto estimates, the model fit, and the testing. In other words it contains the entire analysis of the data. There is, however, one piece of information that can be useful to add in, but that is optional. In reading the kallisto output sleuth has no information about genes, but this can be added allowing for searching and analysis by gene instead of transcript.