8000 --quant-umis, kallisto quant-tcc or bustools count --em? · Issue #67 · pachterlab/kallistobustools · GitHub
[go: up one dir, main page]
More Web Proxy on the site http://driver.im/
Skip to content

--quant-umis, kallisto quant-tcc or bustools count --em? #67

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Open
Miguelb92 opened this issue Apr 28, 2025 · 0 comments
Open

--quant-umis, kallisto quant-tcc or bustools count --em? #67

Miguelb92 opened this issue Apr 28, 2025 · 0 comments

Comments

@Miguelb92
Copy link

Hello, I’m a bit confused about the different options for obtaining transcript-level expression quantifications from single-cell 10x data.

From Sullivan et al. (2024), the recommended workflow is to use kb count followed by kallisto quant-tcc. However, in a previous issue (#288), there was mention of a --quant-umis flag as an alternative for achieving transcript-level quantification.

Could you please clarify the current recommended approach?

Also, I would like to understand better how this differs from using bustools count --em. Are these methods equivalent, or are there important differences I should know depending on the downstream analysis?

Thank you very much in advance for your help!
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@Miguelb92
0