Using DEXseq on kallisto tsv outputs ?

Question

[Gerard]

Hello,

I wanted to know if it is possible to run DEXseq exon analysis from kallisto output abundance.tsv files.

I tried HISAT2 but haven't managed to run it properly yet, so since I have kallisto files that would be a quicker way.

Thank you !

Answer 1

[Gordon Smyth]

Inputting transcript (RNA isoform) quantifications from kallisto into tools like DEXSeq that are designed for exons is not ideal because the transcript quantifications are so overdispersed. The following paper explores this question and shows a better way:

Baldoni PL, Chen L, Li M, Chen Y, Smyth GK (2025). Dividing out quantification uncertainty enables assessment of differential transcript usage with diffSplice. bioRxiv https://doi.org/10.1101/2025.04.07.647659