How distinguish endogenous exogenous genes with scRNAseq data ?
Dear all,
I got data from scRNAseq, 4 different samples : 1 control and 3 treatments. Treatments are overexpression of some TFs by an adenovirus vector. These CMG_genes are cDNA.
After Seurat analyze, we saw we found CMV_genes in control treatment (these genes are not supposed to be there), and the logfold changes were quiet low for treatment samples. So it seems CMV and endogenous genes are not well distinguished and maybe we have a low transduction efficiency.
Is there a way to completely distinguish endogenous and exogenous gene reads?
Thank you in advance.
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sybil-lou •
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Improve transduction efficiency? If the problem is with data quality in the first place, then acquiring better data is the solution. No amount of computational processing is going to turn bad data into good data.
Is this 3'-tagged of full-length scRNA-seq? If 3'-tagged then most reads should map to the last exon which would be the 3-UTR but for overexpressed genes it should be the very part in front of the stop codon, maybe this can help to distinguish it?