Create Task and Run the Pipeline

Procedure

  1. Click the Apps tab to view the apps.

    Note: If the app is highlighted in yellow, an update is available. Select the update link to get the latest app version.

  2. By the BD Rhapsody™ Sequence Analysis Pipeline, click the green play button under Actions. The Task Inputs tab will display the Inputs and App Settings.

Sequence Analysis Pipeline interface:

Complete all required fields (which appear in red), and all desired optional App Settings (may depend on assay).

  1. In the Inputs section, import your files for analysis according to these requirements:

    • For every R1.fastq.gz file, import the paired R2.fastq.gz file. For ATAC-Seq, also include the corresponding index read I2.fastq.gz file.

    • Multiple sequencing libraries can be run together as long as they are from the same set of cells, but the files and libraries can be generated from different sequencer runs.

    • Specify at least one reference for the assay type(s) and species of cells in the experiment.

  2. If necessary, set other input parameters in the App Settings section. For example:

    When using a BD® Single-Cell Multiplexing Kit, be sure to select the Sample_Tags_Version (Single-Cell Multiplex Kit

  • Human, Mouse, or Flex) from the dropdown menu.

    See Pipeline parameters for details on each app setting.

  1. Click Run. Seven Bridges Genomics displays the app running on the Tasks tab.
  2. If you enabled email notifications, look for notification of the completed run.