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Software

My Ion Torrent™ Ion AmpliSeq™ custom design has low predicted coverage; what can I do to improve it?

If you’ve reviewed your design and are not satisfied with the results, please click on the “Not happy with this design? Let us help” link to have an Ion AmpliSeq team member contact you about additional options for your design.

Why do I see the sequence GGCCAAGGCG at the beginning of the majority of the reads in my sequencing data analysis?

The GGCCAAGGCG sequence is part of the RNA library adapter sequence. This sequence can be automatically trimmed by the software by selecting the “RNA_Barcode_None” option under the Barcodes menu. The run can be reanalyzed with the correct barcode settings to trim the adapter sequence. In the future, the “RNA_Barcode_None” option should be selected in the run plan or selected on the instrument prior to starting the sequencing run.

How do I reanalyze my data with a different reference sequence?

Log in to Torrent Browser and click the “Data” tab, “Completed Runs & Reports page”, and find your run name. In the table view, click the “Reanalyze” option in the gear menu on the right of the run entry. The main run analysis dialog opens. Click the “Advanced” button to display the additional run parameter options. Click the “Alignment Reference” pull-down menu and select the reference for this run. (Optional) Change other advanced options if required. (See “Work with Completed Runs” for a description of the advanced fields.) Click the “Start Analysis” button.

How do I change the barcoding set used to analyze a run?

Follow these steps to change the DNA barcode ID:

  • Open a run reports listing in the “Data,” “Completed Runs & Reports”tab.
  • In the list view, click the “Edit” button on the right side of the run listing. The Edit Run window opens. 
  • Click the barcode menu pull-down and choose the correct barcode set. If you have custom barcode sets, your list is different. Click the “Save”button (in the bottom right corner).
  • You can now reanalyze the run from the “Data,” “Completed Runs & Reports”tab.
What are the types of data files and which should be archived?
  • Signal Processing Input—Required to reanalyze an Ion Torrent™ Ion PGM™ or Ion Torrent™ Ion Proton™ run from scratch. (The Output file category is also required.)
  • Basecalling Input—Required to re-analyze an Ion PGM or Ion Proton run from basecalling. (The Output file category is also required.)
  • Output—Required to see the run report in the Torrent Browser and either to reanalyze the run or to launch a plugin.
  • Intermediate—Useful to troubleshoot a run. Not required for the run report or for re-analysis.

Intermediate files can be deleted if not needed for run troubleshooting. Depending on your institution, you may need to keep all other files (Signal Processing, Basecalling, and Output). 

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For Research Use Only. Not for use in diagnostic procedures.