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Questions tagged [cellranger]

For questions regarding use of the 10X Genomics' "Cell Ranger" analysis tool for the Chromium single-cell sequencing platform.

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No counts for added gene in cellranger (scRNA-seq)

I have a set of scRNA-seq samples enriched with FACS for cells expressing a specific gene reporter (TdTomato). In particular the gene I want to report has positive counts in the resulting matrix for ...
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