I have transcript abundances from kallisto run with 100 bootstraps. My understanding is the bootstrapping gives information about the variability in the abundance estimate. If I use tximport to import this abundance information for use in deseq2, is the variance information from bootstrapping used by deseq in any way or does deseq calculate the variance in a different way?
I see in the tximport manual that there is a way to import the inferential replicate values by setting
varReduce to summarize the inferential replicates in to one variance value per transcript. But is this information used by DeSeq2 in anyway during the diff expression analysis?
Also, does RSEM perform any variance calculation for the estimated counts?
Background: I am trying to compare kallisto -> sleuth with featureCounts -> DeSeq2. kallisto followed by sleuth shows no significantly differentially expressed genes (at transcript or gene level) while featureCounts -> DeSeq2 shows several genes that are differentially expressed. To know if this is an effect of having the variance data, I wanted to try running the kallisto transcript abundances in Deseq2.