Import samples

Import Samples from CSV file is an alternative way to populate Sample table and sample-level analysis settings on the Configuration page.

Each CSV template is different depending on the Index Adapter Kit and number of Index Reads. To download a template, first make the appropriate selections in the Run Planning tool then use the Download Template link above the Sample Table.

CSV Template

The CSV template only includes editable columns in the Sample Table and the sample-level analysis settings if applicable (e.g. for RNA Seq application with Differential Expression). Import will auto-populate the derived columns from the input data, e.g. Index names and sequences are derived from the respective Well Position.

• For custom or standard kit with fixed plates:

  • Sample ID*, Well Position*, Project, and sample-level analysis settings (if applicable)

• For custom or standard kit with fixed indexes:

  • If single index strategy is selected: Sample ID*, I7 Index* , Project, and sample-level analysis settings (if applicable)

  • If dual indexes strategy is selected: Sample ID*, I7 Index* , I5 Index*, Project, and sample-level analysis settings (if applicable)

• For Not Specified kit:

  • If single index strategy is selected: Sample ID*, Index 1*, Project, and sample-level analysis settings (if applicable)

  • If dual indexes strategy is selected: Sample ID*, Index 1*, Index 2*, Project, and sample-level analysis settings (if applicable)

Columns marked with asterisks are mandatory.

Import behaviors

• Import will fail if an incorrect CSV template is used (columns do not match the Sample table).

• All rows in the input CSV file will be imported.

• Invalid inputs will result in blank cells in the Sample table.

  • Invalid well position or Index name when custom or standard kit is used

  • Incorrect data type, e.g. string input when a number is expected

  • Out-of-range value

  • Invalid option for a select or dropdown list field

• If there are multiple rows defining the same Sample ID, the sample-level analysis settings must be consistent.

  • If different values are specified, the resulting sample-level analysis settings will be blank.

Lane numbers

For instruments that support loading separate lanes, the CSV template also includes Lanes column.

• Enter one or more lane numbers in this column. When multiple lane numbers are specified, separate the values by commas.

• If a Lanes cell contains an invalid lane number, the resulting cell will be blank.