Question: Normalization read counts scRNA seq with spike ins
gravatar for tetapunto
3.7 years ago by
tetapunto0 wrote:


I'm working with data obtained with sc-RNA seq where we used ERCC spike In to control for transcriptional amplification. I have some troubles with read counts normalization.

My question is: Is it possible to normalize read counts from a cell with the sum of spike ins read counts in that cell?

sequencing rna-seq • 1.4k views
ADD COMMENTlink written 3.7 years ago by tetapunto0

Your question sounds similar to SAMstrt. Maybe you can take a look.

ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by shunyip200
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