comparison of conditions scRNA-seq

Question

[ntsopoul]

Hi,

quick question: I have two data sets scRNA-seq(10x) aligned with cellranger separately (two separate bam files). To load the data in seurat and compare the two data sets, do I need to have them aligned before into one single .bam file via cellranger, or can I combine them later in seurat?

Answer 1

[benformatics]

In Seurat you would be loading a counts matrix (cells x genes) so you don't need the BAM file per se... What you need to be sure of is that they were aligned to the same reference genome/transcriptome and that the counts are tabulated in the same way (whether you use the provided 10x matrices or count them yourself from the BAM files)/