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Wonder if we can learn something about reference mapping here. We have scRNA-seq data form 10x platform. We want to map barcodes to mouse immune cells. When we will use two references, we got very different results regarding fractions of immune cells. Using one reference, we see more macrophages than dendritic cells; using another reference, we see more dendritic cells than dendritic cells. I am sure someone here may have similar experience? What are your opinions or solutions? Thanks.
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM