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Add auto chemistry detection for solving mixture of 10X scRNA-Seq chemistries (alevin, kallisto, star) #388

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wzheng0520 opened this issue Oct 31, 2024 · 2 comments
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enhancement New feature or request

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@wzheng0520
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Description of feature

Hi,

I’d like to implement an auto-detection module to automatically identify the chemistry type for scRNA-seq libraries. This feature would help address scenarios where multiple library chemistries are mixed. By selecting "auto" for the chemistry parameter, the pipeline could perform internal detection to assign the appropriate chemistry type for downstream processing.

Since CellRanger already has an internal function for this, it could also benefit tools like Alevin, Kallisto, and STAR. I’ve developed an internal version based onv2.7.1. Would it be possible to push this as a new branch, or would it be preferable for me to make the updates on the current dev branch to support a future release?

Sincerely
Winnie Zheng

@wzheng0520 wzheng0520 added the enhancement New feature or request label Oct 31, 2024
@grst
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grst commented Oct 31, 2024

Dear @wzheng0520,

if you push this into a branch and make a (draft) PR, I am happy to take a look.
In principle I am open to such a feature, but in the end I'll need to decide if the additional complexity is worth it. It's always a trade-off between adding new features and ensuring the pipeline is maintainable long-term.

@wzheng0520
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Hi @grst

Thanks so much, I will push today and let you know once I completed, so you could take time to review it!

Sincerely
Winnie Zheng

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