Question: spike-in Single cell RNA-seq
gravatar for mikysyc2016
6 months ago by
mikysyc201680 wrote:

Hi all, I need to define control features (genes) - ERCC spike-ins and mitochondrial genes when I do single cell RNA-seq analysis. while isSpike in SingleCellExperiment package defunct now.

isSpike(umi, "ERCC") <- grepl("^ERCC-", rownames(umi))
isSpike(umi, "MT") <- rownames(umi) %in% 
c("ENSG00000198899", "ENSG00000198727", "ENSG00000198888",
"ENSG00000198886", "ENSG00000212907", "ENSG00000198786",
"ENSG00000198695", "ENSG00000198712", "ENSG00000198804",
"ENSG00000198763", "ENSG00000228253", "ENSG00000198938",

Did anyone know how I can do this step in R now? Thanks in advance!

sequencing rna-seq R • 176 views
ADD COMMENTlink modified 6 months ago • written 6 months ago by mikysyc201680
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