hello i have a question , i integrated two data ( 2 samples of B cells) with cell ranger aggr and with filtered matrix data from cell ranger aggr , i apply the seurat script but i dont know how to distingue between my two samples after clustering i can't use split.by because there is no row to use
What software are you trying to use? Either combine with cellranger, or seurat, you don't use both. The Loupe output will know what library each barcode came from.
The barcodes of the aggregated data should all have a number appended to them to indicate which library they came from.
zcat barcodes.tsv.gz | tail TTTCCTCCAAAGAATC-11 TTTGCGCAGCTAACTC-11 TTTGCGCGTACCGGCT-11 TTTGGTTAGCAATATG-11 TTTGGTTCACCGCTAG-11 TTTGGTTCAGGTCTCG-11 TTTGGTTTCCACTGGG-11 TTTGTCAGTACGCACC-11 TTTGTCATCAAGCCTA-11 TTTGTCATCACGAAGG-11
When you integrate with Seurat, you tell it what project name to assign to each sample, and that gets stored in the metadata when you integrate under "orig.ident"
>tail(combined.all[]) orig.ident nCount_RNA nFeature_RNA integrated_snn_res.0.2 seurat_clusters TTTGGTTAGCAATATG-1_5 Untreated 3600 1157 2 2 TTTGGTTCACCGCTAG-1_5 Untreated 3764 1198 2 2 TTTGGTTCAGGTCTCG-1_5 Untreated 1941 679 0 0 TTTGTCAGTACGCACC-1_5 Untreated 5478 1327 2 2 TTTGTCATCACGAAGG-1_5 Untreated 2237 895 4 4