Hi all, This post is about using DESeq2 for DE analysis without replicates. I know that DEseq2 is a tool built for RNA-seq and it needs at least 3 replicates. I just want to analyze scRNA-seq data using DEseq2, but I need help.
I have four samples A,B,C,D and I got 5 clusters each through seurat analysis. (Each samples are pooled with 3 mouse) To describe as a metadata, cluster_id sample_id cell_1 cluster_1 A cell_2 cluster_2 B cell_3 cluster_4 C ... cell_1000 cluster_5 D it would be like this.
What I want to do is 1. Compare the DEGs of samples A and B, and 2. compare cluster_1 and cluster_2 in A.
At this time, if the number of cells corresponding to sample A is 300, I want to divide 300 cells into 100 pieces and make them A_1, A_2, and A_3 for DESeq2(I think it would be a pseudo-replicate if I gave it a name, and the count matrix is dgCMatrix (Sparse matrix)).
Can you give me a solution for this? Even if it's not DESeq2, please let me know if there is another way. Thank you very much for your help.
