how should I merge the matrix data？

1

I have six single-cell RNA-seq datasets, each generated from different samples. I would like to merge them into a single dataset for integrated downstream analysis (e.g., clustering, visualization, batch correction).

Should I combine them into one file before uploading to Galaxy? Or is there a recommended way to merge them directly within Galaxy using existing tools or workflows?

Also, what is the best format to use for merging—should I convert each dataset to .h5ad first（Import Anndata）, or can I work directly with .mtx files?

Thanks in advance for your help!

2

Would Hands-on: Combining single cell datasets after pre-processing / Combining single cell datasets after pre-processing / Single Cell help you? This tutorial is part of a series so make sure you also check out the rest of Single Cell / Tutorial List.