10X Chromium 5' gene expression

Skip to first unread message


Sep 20, 2018, 9:22:25 PM9/20/18
to kallisto-sleuth users
Hi all,

I have tried out the kallisto scRNA TCC prep tool for 10X Chromium 3’ digital expression data. Is it possible to adapt it for 10x single cell 5' sequencing data? What would I have to change?


Sundar Gadepalli

Mar 30, 2023, 11:25:50 AMMar 30
to kallisto and applications
Hello Rachel,
I;m trying to run Kallisto on 10x 3' ScRNA seq data. However, unable to get the TCC matrix. SInce, you said you were able to successfully create TCC matrix, would. you mind to share your pipeline or publication that talks about its implentation? I'm trying to  perform a differential isoform analysis. Any suggestions would be helpful. 

Rachel Ng

Mar 30, 2023, 4:55:49 PMMar 30
to kallisto and applications

Have you tried the code from this repository?

Rachel Ng

Mar 30, 2023, 5:08:15 PMMar 30
to kallisto and applications
Actually, it looks like their newest kallisto bustools can output TCC.
According to the documentation here, you can use the `--tcc` option.

I have not ran kallisto since they created this new bustools so I don't know if it works with 10x 3' scRNA. But according to this paper from Pachter lab, they are able to get TCC for a 10x 3' dataset in this analysis.

Reply all
Reply to author
0 new messages