Used featureCounts to generate a count matrix for sc RNA-seq and it has all 0s.

Question

[Shay]

Hi,

I've been using featureCounts to generate a count matrix for my scRNA-seq data, but it's showing all zeros. I'm a bit puzzled as to why that might be happening.

I'd really appreciate any assistance with this.

[GenoMax]

What kind of scRNAseq data?

[Shay]

It is gene expression data

[GenoMax]

But is it 10x or some other type of single cell data. Depending on the answer featureCounts may not be the right tool.

[Shay]

Since I am not dealing with 10x data this time around, cell ranger wasn't used. I opted to use featureCounts, which came highly recommended by experienced bioinformaticians in my lab. Hope that clears things up :)

[GenoMax]

Then it may be easier to consult with the local experts since you can show them your command lines/data/result. There is not enough information here to help you, unless you provide additional details.