Question: DE analysis of single cell RNAseq
gravatar for alirezamomeni707
4 weeks ago by
alirezamomeni7070 wrote:

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?

rna-seq • 110 views
ADD COMMENTlink modified 4 weeks ago by kennethcondon2007750 • written 4 weeks ago by alirezamomeni7070

Is this 10x single cell RNAseq data?

ADD REPLYlink written 4 weeks ago by genomax29k

Maybe you can use DESeq2 with your ReadCounts.

ADD REPLYlink written 4 weeks ago by zjhzwang180

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.

ADD REPLYlink written 4 weeks ago by russhh2.4k
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