Single cell Sequencing

Question

[Bioinfo]

Hello,

I have two question

In single cell sequencing, I have two set of data , Droplet and FACS. In droplet I have 3 data (barcode, genes and matrix) and in Facs, I have counts

How are they related?

I can create my data using R from droplet

counts <- readMM("matrix.mtx")
genes <- read_tsv("genes.tsv", col_names = FALSE)
gene_ids <- genes$X1
cell_ids <- read_tsv("barcodes.tsv", col_names = FALSE)$X1
rownames(counts) <- gene_ids
colnames(counts) <- cell_ids

but when I want to annotate the FACS, I am facing problems I know each column is a cell and each row is a cell but how can I annotate it? I am more interested to have a matrix each column being a cell and and each row a gene. I dont want to use fancy package, anyone knows basic R?

this is an example of the FACS

df< -structure(list(X = c("0610005C13Rik", "0610007C21Rik", "0610007L01Rik"
), A14.MAA000545.3_8_M.1.1 = c(0L, 1L, 0L), E1.MAA000545.3_8_M.1.1 = c(0L, 
0L, 0L), M4.MAA000545.3_8_M.1.1 = c(0L, 0L, 0L)), row.names = c(NA, 
3L), class = "data.frame")

Answer 1

[abedkurdi10]

If I understand you well, you mean you want to annotate cells using some basics R. I don't think this is possible. Check Seurat package for example. it allows you to analyze and annotated the found cluster.