Question: DE analysis of single cell RNAseq
gravatar for alirezamomeni707
4 days 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 • 86 views
ADD COMMENTlink modified 4 days ago by kennethcondon2007530 • written 4 days ago by alirezamomeni7070

Is this 10x single cell RNAseq data?

ADD REPLYlink written 4 days ago by genomax27k

Maybe you can use DESeq2 with your ReadCounts.

ADD REPLYlink written 4 days ago by zjhzwang160

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 days ago by russhh2.2k
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