Can someone recommend and method/way to calculate a proper number of cells for NGS? E.g. let's say we know that in the experiment we have 1 out of 2000 with a variant, and it is not present in the control. How many cells need to be taken for single cell NGS to detect the variant with 95% CI?
It is hard to provide a specific answer without knowing the actual platform you are using. In general, this will be dependent on other factors including whether dual index UMI adapters are used and your target sequencing depth.
Hi Dmitry Klokov
what a good question, but I'm afraid that scRNAseq could not be the solution. since most of popular techniques to obtain single cells provide limited number of cells (7000 for 10xgenomics per sample) and your variation frequency is up to 1/4000 (allele frequency), I would advice you to test the variation directly on extracted DNA and targeted NGS, knowing that 1ng of DNA can represent 150 individual cells (in human). very rare variants are indeed very hard to screen.
fred
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