Number of genes/transcript detected in scRNA seq
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6.0 years ago
naman.sep • 0

Hi

I am new to scRNA seq and am interested to know how to find the threshold for number of genes that i should expect in single cells. I am getting wide range from ~1600 per cell to around 4000 per cells. I am already considering cells with more than 2500 genes to be doublets. Most of my cells have less than 2000 genes. IS there any way how i can decide the threshold and to exclude the cells with more genes:

Methods: Smart-seq2

I decided to call gene present or absent if TPM>1.

Any help in this regard would be deeply appreciated.

Regards

RNA-Seq scRNA-seq gene • 1.3k views
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