Chris Kang

Calculation of MT and RP portion: ```{r} seo[["percent.mt"]]

> Which workflow are you using to go from the BUS file to a gene count matrix compatible with seurat? Somewhere in the translation the names might be messed up...

Hi, I re ran the analysis using the latest version of kallisto. looks like this time Mt genes are preserved, but HLA's are eliminated.  This is 10X PBMC data,...

Hi, just writing to ask if you guys have identified the problem...

Yes, this ENST is indeed in the fasta, and not in the gtf (both downloaded from ensembl). I agree this seems to be a gene id problem... It'll be great...

Thanks for the encouragement Lucas! I didn’t encounter this problem during my tests, looks odd... It is definitely not related to the number of HVGs though, in my case I...

Regarding time consumption, if you choose to input all the genes (g) but subset with hvgs (h), the algorithm will run twice (m\*n\*g + m\*n\*h, m=batch 1, n=batch 2), because...

Hi Lucas, could you update to 0.1.9.3 and check if the error occurs? Thank you!

Will fix it soon

Yes, this means the cython fails. In this case, the program still work but will take much more time and memory, since it's now running in python. If your sample...