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scRNAseq - Threshold to call a cell highly expressing a particular gene

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  • scRNAseq - Threshold to call a cell highly expressing a particular gene

    Hi. Novice user here.
    I am looking at expression values of scRNAseq data using UCSC Cell Browser. I can display the heat map of expression values, which bins cells into percentile ranges.
    Are there any best practice rules for selecting a percentile threshold to call a cell "highly expressing"? I have been using top 25%, but this is arbitrary. For example I would like to determine how many cells are both in S phase and highly expressing Gene X.
    Thanks!
    Last edited by silvam; 08-20-2022, 12:48 PM.
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