comparison of conditions scRNA-seq
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9 weeks ago
ntsopoul ▴ 10

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?

scRNA-seq seurat 10x • 147 views
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Entering edit mode
9 weeks ago

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)/

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