Adding new samples to single cell rna-seq analysis
Hi,
This might be a very simple and a beginner question.
I have 6 10X scRNA_seq samples (control and treatment1) and have performed the QC and downstream analysis on them. We just sequenced 2 new single cell scRNAseq samples (10X chemistry) with different treatment (treatment2). Can I just perform QC on the new data and combine the Seurat objs of 6 and 2 samples and then perform clustering and if needed, perform batch effect or it is just impossible to even combine the two sets of data with different treatments?
1 answer
luckily the CellRanger software has built-in programs to do exactly this. check out the aggregate function as a starting point
Log in to answer this question.
More posts like this
-
Iterative clustering with silhouette score
written by sleepystudent •
-
issue with merging single cell data files
written by Sara
-
Question: should we integrate samples from different study groups?
written by mengjieqiu1996 •
-
Geom_bar plot with several x-axis variables
written by sking •
-
SCTransform prior or after merging samples into one object?
written by annadv •
-
recommendation needed: scRNA-seq batch effect correction methods that can be used for differential …
written by changxu.fan
-
How distinguish endogenous exogenous genes with scRNAseq data ?
written by sybil-lou •
-
Calculating differential expression genes between two sample sequenced using 10x
written by singcell •
-
RNA-seq batch effect correction
written by endikavarela •
-
RNA-seq unbalanced batch effect correction
written by endikavarela •
