What is a count matrix for input into Seurat supposed to look like?

Hello,

I hope you are safe and well.

Could someone share what a count matrix for input into Seurat is supposed to look like?

I have count matrices however they each cells count matrix is in a separate file.

This is the data I want to analyze in Monocle 3: www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2978831 The files I’m looking at are in the Supplementary section.

I was guided to aggregate these files into one count matrix file and then bring it in Seurat to normalize it. Then, from Seurat, transform the normalised data and use it as input to Monocle.

This is what I have used to aggregate the data:

> setwd ("~/Desktop/GSE110154_RAW/csv/")
> files <- list.files(path="~/Desktop/GSE110154_RAW/csv/")
> genes <- read.table(files[1], header=FALSE, sep=",")[,1]
> df    <- do.call(cbind,lapply(files,function(fn)read.table(fn,header=FALSE, sep=",")[,2]))
> df    <- cbind(genes,df)
> head (df)

which results in:

     genes                                                                   
[1,] "1/2-SBSRNA4" "0" "0"  "0" "0"   "0" "0"   "3" "0"   "77" "0"   "0"  "0"
[2,] "A1BG"        "0" "0"  "0" "58"  "0" "0"   "0" "0"   "0"  "0"   "0"  "0"
[3,] "A1BG-AS1"    "0" "38" "0" "0"   "0" "0"   "0" "0"   "0"  "0"   "0"  "0"
[4,] "A1CF"        "0" "8"  "0" "123" "8" "418" "0" "144" "0"  "108" "21" "0"
[5,] "A2LD1"       "0" "0"  "0" "0"   "0" "0"   "0" "0"   "0"  "0"   "12" "0"
[6,] "A2M"         "0" "0"  "0" "0"   "0" "0"   "0" "0"   "0"  "0"   "0"  "0"

and then to write the files I did:

> write.table(df, "~/Desktop/GSE110154_RAW/df4.csv", row.names = F, col.names=F, sep = ",")

which results in:

    "1/2-SBSRNA4","0","0","0","0","0","0","3","0","77","0","0","0","0","3","0","0","1","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","7","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","5","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","22","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","2","0","0","0","0","0","38","0","0","0","3","0","0",...
    "A1BG","0","0","0","58","0","0","0","0","0","0","0","0","0","10","0","0","0","0","0","0","0","0","0","0","0","23","0","0","0","0","0","0","0","0","0","3","0","0","0","0","0","0","0","0","0","0","10","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","2","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","14","0","0","2","35","0","0","0","0","0","40","0","0","0","0","0","0","0","26","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","6","0","0","0","0","0","0","0","11","0","0","0","0","0","38","0","0","0","0","0","0","42","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0","30","0","0","0","0","0","0","0","0","0","0","0","0","0","13","0","0","0","0","0","0","18","0","0","0","0","0","0","0","0","0","0","0","0","0","0","0",...
etc...

I’m just not quite sure what a Seurat count matrix is supposed to look like?

I also need to find a good tutorial on how to input this data into Seurat afterwards, normalize and transform it, to input into Monocle3.

I would greatly appreciate anyones help!

Very Respectfully,
Pratik

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