recalculate stats and another filtering step #769
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sjspielman
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May 29, 2024
Co-authored-by: Stephanie Spielman <[email protected]>
sjspielman
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May 29, 2024
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Closes #768
To avoid the negative size factors after filtering (which it turns out had been there for a while), I added a step where we recalculate the per-cell stats and re-filter. It turns out that removing some of the lowly expressed genes created cells with very low total UMI counts remaining, which affected the results. The total number of cells affected was only about 5, but I think it is a nice illustration of some of the unexpected effects of filtering!