differential gene expression using sleuth

Question

[frida.danielsson]

Hi,

I'm currently using sleuth to test for differential expression of transcripts and I wonder if and how it would be possible to "lift up" the results to gene level to see what genes are differentially expressed when still considering variations of transcripts within the same gene?

/Frida

Answer 1

[Thibault D.]

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

[frida.danielsson]

I meant more if it is possible to do it in sleuth?

[Thibault D.]

I don't understand. Would you like to display your differential gene expression analysis with Sleuth style, or to perform this differential gene expression analysis with Sleuth, or ... ?

[frida.danielsson]

Yes, I wondered if there some built in function for doing it in sleuth, looking at DE genes instead of transcripts I mean.

[Thibault D.]

I don't think so, I can not find anything within Sleuth to perform this kind of analysis.

Answer 2

[cpcantalapiedra]

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.