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Sample table

A sample barcode table file is used to list the samples included in an analysis run and optional sample-specific analysis parameters. Each sample in the workflow is defined by its set of well positions on the RT plate. For example, cells from Donor1 were fixed and loaded into the first column of the RT plate. That first column, 1A-1H, would then define the "Donor1" sample in the sample barcode table.

A set of examples for the different Quantum RNA configurations is included in docs/examples/quantum-sample-barcode-tables. It is a comma separated file (csv), with a header line (column names), followed by one sample per line. The first column is required to be sample and contains the name of each sample. All other columns are optional.

Column Description Example
sample Sample name PBMC-2
barcodes RT-plate wells used for this sample 1A-2H
libIndex2 PCR indices (semicolon separated) used for this experiment (optional) QSR-1;QSR-2
expectedCells Approximate number of cells in this sample (optional) 50000

Note

  • sample should consist only of letters, numbers and dashes (-) and start with a letter
  • barcodes is optional if only a single sample was run. In that case all RT wells will be grouped together
  • libIndex2 is optional. If it is left out, the workflow will search for all possible PCR indicies in the input data
    • For data generated with the Scale RNA v1.1 kit, users should provide a libIndex column instead; for example "RNA-A-AP1"
  • expectedCells is optional. If it is left out or set to 0, the number will be estimated from the read count distribution

Sample Barcodes

If multiple samples were included in the experiment, they are effectively pooled in the sequencing library, and the analysis workflow will demultiplex them based on the sample (RT) barcodes. E.g

sample barcodes
Foo 1A-6H
Bar 7A-12H

The RT wells used for each sample are given in barcodes as either

  • An individual value (1A)
  • A range of wells (1A-2H)
    • Wells are sorted first by number then by letter, i.e. 1A-1H.
    • Note that all ranges are read in column-wise order; e.g. 1A-2C, refers to 1A-1H (all of column 1) plus 2A-2C.
  • A list of values or ranges, separated by semicolon (;) (1A;2A-2D)