Marker genes for a cell type in ScRNA

Question

[rob.costa1234]

In single-cell RNA-seq. if I have to assign marker genes to a specific cell type. To do so- That marker gene will be present only in one cluster of one cell type and not any other cell type? Do we see the relative expression of marker genes and if that gene is upregulated in one cluster, that may be the case if gene is present in more than one cell type. In that case we cannot assign that particular gene as a marker gene for that particular cell. Is there any standard benchmark in this direction? Any feedback

Answer 1

[igor]

There is no standard. The robustness of your marker genes will be dependent on your dataset. If you have genes that are detected in only one cluster, that is great, but that is rare unless your clusters are very distinct. However, if you have genes that are only 10% higher in one cluster than another, that may also be acceptable.