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Missing valid cells #255

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CFrangieh opened this issue Mar 14, 2020 · 0 comments
Open

Missing valid cells #255

CFrangieh opened this issue Mar 14, 2020 · 0 comments

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@CFrangieh
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Hi. I am experiencing the error "WARNING - No ambient RNA beads were found; maybe sample had too few cells?" when running loompy fromq (uses kallisto for alignment). I know the sample has ~10,000 cells from processing it with cellranger and examining the fastq files directly, and kallisto successfully aligns several other samples from the same flowcell. Do you have any suggestions for how to proceed?
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@CFrangieh