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scRNA-seq quality control

Sam Morabito

21 October 2021

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Quality control reports

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Cell Ranger quality report (human prefrontal cortex)

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What should a “good” barcode rank (knee) plot look like?

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Cell Ranger quality report (human prefrontal cortex)

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Cell Ranger quality report (human prefrontal cortex)

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Cell Ranger quality report (mouse habenula)

sample_name

alerts

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Cell Ranger quality report (summary)

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Cell Ranger quality report (summary)

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Cell Ranger quality report (summary)

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split-pipe quality report (human prefrontal cortex)

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split-pipe quality report (human prefrontal cortex)

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split-pipe quality report (human prefrontal cortex)

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Empty drops algorithm

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Running cellbender remove-background

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Running cellbender remove-background

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Running cellbender remove-background

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cellbender versus alternative methods

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before cellbender ambient RNA removal

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after cellbender ambient RNA removal

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Doublet detection

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Overview of Scrublet algorithm

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Evaluating Scrublet using genotyped data as ground-truth

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Evaluating Scrublet on differentiating cell trajectory

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Visualizing predicted doublets

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Predicted doublets versus singlets

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Dealing with the cell-cycle

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Variability due to cell-cycle genes

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Variability caused by cell-cycle can be ‘regressed out’

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Filtering based on UMI / genes

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https://tinyurl.com/genpals-qc

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Unique molecular identifiers (UMIs) are sequences in each FASTQ read that help control for PCR duplicates

  • UMIs are sequences often added at the same time as barcodes during library preparation�
  • Finding and collapsing reads with the same UMI help negate amplification bias from PCR �
  • UMI sequences for 5bp UMI�

ResearchGate