Hello All,

I have generated spliced and unspliced matrices using kallisto bustools (lamanno). My question is that the unspliced matrix is similar to the count matrix obtained from pre-mRNA and the spliced count matrix is similar to mRNA?

If so, Then can I use the unspliced count matrix for DEG analysis

Please help me !!!

Thanks

Thanks for your reply. Maybe my question is very naive. Previously i quantified using cell ranger pipeline I am new to kallistobustools. I have quantified the counts (Kallisto bustools) spliced, unspliced region. Now, i would like to preprocess the counts and do typical integration, and clustering followed by DEG analysis and RNA velocity.

adata.h5ad --> counts present in spliced and unspliced region

layers spliced--> sparse matrix spliced count matrix

layers unspliced --> sparse matrix unspliced count matrix.

Please help me !!!

Thanks Akila