DE analysis of single cell RNAseq

Question

[alirezamomeni707]

I have scRNAseq data (counts files not fastq files). I got 3 types of counts including:

1- BarcodeCounts
2- ReadCounts
3- TranscriptCounts

now I want to do differentially expression analysis to identify DE genes. for normal RNAseq we ususally use read counts to identify significant genes. do you know which of these files must be used for single cell RNAseq for DE analysis?

[GenoMax]

Is this 10x single cell RNAseq data?

[zjhzwang]

Maybe you can use DESeq2 with your ReadCounts.

[russhh]

You have to know what your contrast will be before you attempt this. If you are both defining cellular subsets on the single-cell data and then trying to do differential expression between those cellular subsets, it's not very good practise.