Check my understanding – difference between number of reads sequenced and Seurat nCount_RNA

Check my understanding – difference between number of reads sequenced and Seurat nCount_RNA

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I am reading a publication which has sequenced the 10x scRNA-seq library to around 50,000-100,000 reads / cell. When I performed QC and checked the nCount_RNA metric, the median nCount_RNA across all samples is around 3600.

Since nCount_RNA is the number of detected molecules (UMIs)/ cell, I presume the large difference in the number of reads / cell vs the number of detected molecules / cell, is that a lot of the reads are PCR duplicated (share the same UMIs). Would this be a correct interpretation of the discrepancy? I also presume that these numbers are typical of an scRNA-seq library.


scRNAseq

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