Using log2(TPM/10+1) values in Seurat

Question

[zizigolu]

Hi

I have downloaded log2(TPM/10+1) values of 10X Malignant ascites single cell from GSE146026 as raw data is not available

Is there anyway to use this matrix and convert that to a Seurat object?

Thank you so much for any idea

Answer 1

[fracarb8]

Starting with raw counts it's advised, but not required. You can pass your TPM matrix to CreateSeuratObject, but you need to skip the normalisation steps, as you already have the log counts. After that, you can procede with scaling (beware of the warnings if you want to do it) and the rest...

[zizigolu]

Sorry you can help with this question please?

https://bioinformatics.stackexchange.com/questions/15948/making-seurat-object-from-a-processed-file

I want to make Seurat object having all of cell barcodes, genes, patients ID but I really can not find the answer

[fracarb8]

Read10X reads 10x output folders, and it requires the content to be exactly what it is supposed to be output by cellranger (i.e. the triad of files features, barcodes, matrix). If you are providing your own matrix you need to CreateSeuratObject(counts = yourMatrix). Just make sure that you have genes and cellsID as rownames and colnames.