Extracting Transcript-Level Counts from Single-Nuclei Data for DTE/DTU Analysis

[AkilaRanjith]

Hello,

I have quantified gene counts from single-nuclei data using kallistobustools. The pipeline merges transcript counts into gene counts, but I would like to analyze transcript-level proportional changes between conditions (DTE/DTU analysis).

Is there a way to extract transcript counts from the bus file? Additionally, how can I use the transcript counts to analyze transcript expression changes with DESeq2 or limma? Are tools like DEXseq or Saturn compatible with this analysis for DTU?

I have merged all the data and annotated the cell types, with gene counts and cells in a single h5ad file. Is there a way to retrieve the transcript counts from the original bus file and identify changes in transcript expression? else i need to run the count using different methods?

Can you guide me on this?

Thanks,
Akila