DE analysis of single cell RNAseq
0
0
Entering edit mode
4.4 years ago

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

1- BarcodeCounts
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?

RNA-Seq • 1.6k views
0
Entering edit mode

Is this 10x single cell RNAseq data?

0
Entering edit mode

0
Entering edit mode

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.