MengjunWu
MengjunWu
Hi, Following this question, I want to ask how do you collapse UMI to generate cell x transcript equivalence class count table if pseudoaligned reads to transcripts? Do you still...
Many thanks! To confirm if I understood correctly: In your first example: the two UMI sequences are two different reads, i.e. UMI sequence ATCG: tx 0, tx 1 (read1) UMI...
@mschilli87 Thanks a lot for the alternative scenario! Got it and I think it makes sense.
Thanks for the reply! 1. Yes, I am running on a single sample, with/without cluster mode 2&3. Yes, I am running the same random seed, here are the code and...
Another thing I noticed is dbr.per1K is to some extent insensitive to the value passed to it. I tried both 0.004 and default 0.008, the percentage of doublet removed are...
Many thanks for the detailed reply! The idea of ceiling is to always take slightly larger doublet rate compared to the exactly doublet rate to be more conservative. (Also as...