Yenaled
commented
1 month ago I'll be honest: I've never actually analyzed MARS-seq data.
From what I can find online, it seems like R2 contains a 7-bp barcode + 8-bp UMI, while R1 has a 4-bp barcode after the first 3 nucleotides, then those 7 bp's are followed by the sequence to be mapped.
If this is the case, then the technology string will be:
-x 0,3,7,1,0,7:1,7,15:0,7,0
This means take the 4-bp barcode of R1 concatenated with the 7-bp barcode of R2, extract the 8-bp UMI from R2, and extract the sequence-to-be-mapped from R1.
What is important to have is the list of barcodes provided by the assay. I can't provide that for you since it's experiment-specific. The list of barcodes provided should be the 4-bp (pool) barcode followed by the 7-bp (cell) barcode
github-actions[bot]
Hi, I have been using kb-python to analyze scRNA-seq. first, thanks for creating such a user-friendly and useful tool. I appreciate it! I just had a technical issue when reanalyzing scRNA-seq in this paper by Lau et al in which they have used MARS-seq. My question is that when I wanted to run kb count , I couldn't figure out what would the best code to use to specify umi/barcos of the mars-seq (-x). I couldn't find mars-seq when I ran kb --list and i tried a few codes but was not successful. I was hoping that you may have encountered this issue before or may have already a solution for it. Thanks! ps I accidentally posted this very same comment for kallisto too.