Compatibility with Seurat and SingleCellExperiment objects

[katsikora]

Hi,

is there a way to apply purge_phantoms on a Seurat or SingleCellExperiment class object?
Converting from these to .h5 in R is a bit of a headache.
Or would you have another way to make it work with native STARsolo output?

Best,

Katarzyna

[rfarouni]

Hi Katarzyna,

The UMI x Cell count matrix output can be converted into a Seurat of SCE object as this example example shows but you cannot start with these objects because the method needs to combine into one table the read counts -not the UMI counts -for all samples run on the same lane. As for now, only the output of Cellranger can be loaded by the software. That said, you don't necessarily need to convert the files to .h5 format if you can instead manage to read the data into R and make sure it has the same structure as in the first step of the workflow out <- read10xMolInfoSamples(samples_filepaths). Then you can just skip the first step and run the rest of the workflow from there.

Rick,

[katsikora]

Hi Rick,

I see, thanks for the clarification!

Best,

Katarzyna