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v1_0.md

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Overview

We expect a quality_control HDF5 group at the root of the file, containing parameters and statistics for quality control on the RNA count matrix. The group itself contains the parameters and results subgroups.

Definitions:

  • num_cells: number of cells in the dataset, prior to any filtering. This is typically determined from the inputs step.
  • num_samples: number of samples in the dataset. This is typically determined from the inputs step.

Parameters

parameters should contain:

  • use_mito_default: a scalar integer to be interpreted as a boolean. This specifies whether to use the default mitochondrial gene list.
  • mito_prefix: a scalar string containing the expected prefix for mitochondrial gene symbols.
  • nmads: a scalar float specifying the number of MADs to use to define the QC thresholds.

Results

results should contain:

  • metrics, a group containing per-cell QC metrics derived from the RNA count data. This contains:
    • sums: a float dataset of length equal to num_cells, containing the total count for each cell.
    • detected: an integer dataset of length equal to num_cells, containing the total number of detected genes for each cell.
    • proportion: a float dataset of length equal to num_cells, containing the percentage of counts in (mitochondrial) genes.
  • thresholds, a group containing thresholds on the metrics for each batch. This contains:
    • sums: a float dataset of length equal to num_samples, containing the total count threshold for each batch.
    • detected: an integer dataset of length equal to num_samples, containing the threshold on the total number of detected genes for each batch.
    • proportion: a float dataset of length equal to num_samples, containing the threshold on the percentage of counts in (mitochondrial) genes for each batch.
  • discards: an integer dataset of length equal to num_cells. Each value is interpreted as a boolean and specifies whether the corresponding cell would be discarded by the RNA-based filter thresholds.

History

Added in version 1.0.