Using removeSwappedDrops for cellranger reanalysis output (without molecule_info.h5)

[ayumatsubo]

I used cellranger reanalyze protocol (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ra) and cellranger reanalyze output does not include molecule_info.h5.

I tried to use removeSwappedDrops function, but I did not know what to set for inputs.

If I set for inputs as molecule_info.h5 from cellranger count for swappedDrops, it may output the matrix that did not process by cellranger reanalyze, right?

I want to set for inputs as read10xCounts(filtered_feature_bc_matrix) for removeSwappedDrops, but I do not know umis, genes, nreads in the SCE object.

Is there any solution after cellranger reanalyze to use SwappedDrops?

Thank you for advance.

[jonathangriffiths]

Hi,

The cellranger reanalyze commands apparently only:

reruns secondary analysis performed on the feature-barcode matrix (dimensionality reduction, clustering, and visualization) using different parameter settings.

This implies to me that there is no change to the underlying data (count matrix) between your cellranger count and reanalyze run. Assuming you are going to be doing QC, dimensionality reduction etc. yourself, you should have no need for the reanalyze output for your swappedDrops analyses, and should be safe to use the count matrix from cellranger count.

Jonny

[ayumatsubo]

I'm sorry to be late to response.

Thank you for quick reply!