Combine a sample that is run in two lanes by the Seurat objects

Question

[Mehrdad Zandigohar]

I have the scRNA data (matrix, features, and barcodes) of a sample run into two lanes L1 and L2:

sample_L1

sample_L2

I created two Seurat objects with Read10X() and CreateSeuratObject() because I had 2 separate matrices, features, and barcodes. Do I just have to use the merge() function to make one final Seurat object if I want one? Also, I filtered each object separately and then merged them. Not sure if that is the correct way of doing it.

Any help would be appreciated.

Answer 1

[rpolicastro]

As a general note, you can merge the fastq files from different lanes before analysis, and some software such as cell ranger can handle multiple fastq files per sample automatically.

For your data you can just merge the seurat objects, and then make a column in the metadata with the new factor levels. Also, the same filtering parameters should be applied to each lane, or you can do the filtering after merging instead.

[Mehrdad Zandigohar]

Thank you Robert for your answer. About "then make a column in the metadata with the new factor levels", do you mean I make factor levels 'L1' and 'L2'?