Secondary analysis of cellranger multi data - which files to use?

Question

[Kevin]

The cellranger multi output comes with 2 main data folders, "multi" and "per_sample_outs". The multi folder has the raw output (cells and background) and the per_sample_outs folder has the filtered output (cells only).

I believe the filtered output is what should be used for secondary analysis with Seurat but wanted to confirm this. I'm also curious about what cases (if any) would the raw output would be preferred?

Answer 1

[Istvan Albert]

I believe that the raw data is mainly used to troubleshoot if something goes wrong along the way; the distributions would be way off.

https://kb.10xgenomics.com/hc/en-us/articles/360001892491-What-is-the-difference-between-the-filtered-and-raw-gene-barcode-matrix-

[GenoMax]

Raw data may also be usable with other packages like alevin.