I have been trying to understand the Seurat for analysing scRNA-seq data. It comes to my mind that the main data is organised in the Seurat object with rows as genes and columns as the cells, and the entries are the gene read count.

I am confused with the statement, "the connection between the detected genes in the cells and the read counts".

What is exactly the meaning of the detected genes in the cells biologically and its connection to the read counts? Can we say if the read count of gene A is 10 it means this gene is detected 10 times in a cell? How to interpret the detected genes biologically?

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    $\begingroup$ This needs more focus and a reference / context of that quote. $\endgroup$
    – ATpoint
    Jun 20 at 16:19

Answer from @ATpoint, converted from comment:

A detected gene is one that has a count > 0, and generally the deeper you sequence the more genes you detect until you reach a saturation which is being influenced by the number of biologically-expressed genes and the single-cell technology you're using, e.g. droplet vs plate-based and the library setup, e.g. end-tagged vs full length.

Counts cannot influence the nature of gene translation. A count is an observation; a translated gene sequence is a physical thing. Whether or not a gene can be translated into protein has no relationship to how often it is observed in existence.

Even with count zero (i.e. no detection in scRNA-seq), it does not mean that the gene is not present in the cell. NGS technology is a relative quantification, I doubt it is meaningful to try to directly make statements about the connection between read counts and biological meaning in the cell.


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