Description
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