Combine aligned reads from multiple run reports

If you are running an application that requires better coverage than the coverage provided by a single chip, you can:

  • run multiple chips with the same sample and library

  • combine aligned reads from multiple sequencing reports

    The combined aligned reads can be treated the same way as results from a single run. For example, it can be exported or used as an input for a plugin.

  1. In the Data tab, click Projects to see the list of projects.
  2. Select a project in the list to view the result sets in the project.
  3. Select the result set or sets that you want to combine into a single run result set.
  4. Click Combine Selected > Combine Alignments.
  5. In the Combine Selected dialog box, enter a new report name.
  6. Make appropriate selections:

    Option

    Description

    Mark as duplicate

    Select this to identify duplicate reads and mark them in the BAM file.

    For some applications, duplicate reads coming from PCR cause problems in downstream analysis. The presence of duplicate reads can create the appearance of multiple independent reads supporting a particular interpretation, when some reads are in fact duplicates of each other with no additional evidence for the interpretation.

    Note: Marking duplicate reads is not appropriate for Ion AmpliSeq™ data, because many independent reads are expected to share 5' alignment position and 3' adapter flow as each other. Marking duplicates on an Ion AmpliSeq™ run risks inappropriately flagging many reads that are in fact independent of one another.

    Overwrite sample name

    Select this to identify duplicate names in your combined samples so that you can rename them.

  7. Click Launch.
  8. (Optional) Click Report to open the summary of the report, or Log to open the log for the report.

The combined report is added to the project from which the combine action was run.

Related Topics
Parent topic: Organize run results with projects