best practices for RAD/collate/quant and file alignment

[lilyzhou222]

Dear team, I’m new to alevin-fry. If I want to reproduce the paper’s cell clustering and annotation, aside from matching the paper’s genome/annotation, is there anything I should do specifically in the RAD generation, collate, or quant steps? Are there particular references or files (e.g., splici build, t2g mapping, chemistry/permit list) that I must align with to ensure downstream clustering/annotation is consistent?

[DongzeHE]

Hi @lilyzhou222 ,

If you are talking about the alevin-fry paper, please refer to our repo for making the results here https://github.com/COMBINE-lab/alevin-fry-paper-scripts

If you are talking about the best practices in general, please refer to the real world example part in the Single-cell Best Practices book https://www.sc-best-practices.org/introduction/raw_data_processing.html#a-real-world-example.

Best,
Dongze