References Management Guide

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Torrent Suite Software space on Ion Community

References Management Guide TOC

References Management Guide

Use the Admin References tab to enter nucleotide sequence Test Fragments , Reference Genomes for aligning reads, and DNA Barcodes for barcode set management.

Access the References tab from the Admin gear menu (near the top right of a Torrent Browser page), with the References option:

The main reference management page opens:

In this page you can click into reference details, download a reference file from your Torrent server, add a new reference, or use the navigation tabs on the left:

• Reference Sequences The main reference management page (shown above).
• Obsolete Reference Sequence s Lists references that need to be reindexed before use. Reindexing is required only on releases that involve a TMAP index change.
• Target Regions Analysis is restricted to only the regions of interest that you specify in this file.
• Hotspots Variant Caller output files include these positions whether or not a variant is called, and include evidence for a variant and the filtering thresholds that disqualified a variant candidate.
• Test Fragments Known sequences used to monitor system characteristics.
• Barcodes Work with Ion barcode sets or your own custom barcodes sets.
  
  
• Upload History Shows the recent uploads of target regions, hotspots, and ampliseq.com zip files:
  
  
  
  
  
  The on a file name to go to its details page (see Target Regions Files and Hotspot Files ). The Status column shows any error results.

Rebuild warning

This warning often appears in the References tab:

This warning appears if your server has references listed in the Obsolete References section. Your action in response to this warning depends on your particular upgrade scenario and obsolete references situation:

• If you upgrade from release 2.2 or higher to 4.x, you do not need to rebuild your reference indices.
• If you upgrade from a release earlier than 2.2, you must rebuild your reference indices after the first upgrade to a 3.x or 4.x release (and before using the upgraded server for analyses).

Reference pages

The following pages describe how to manage your references and related files:

• Update Reference Library Indexes
• Upload a New Reference File
• Delete a Reference Sequence
• Target Regions Files and Hotspot Files
• Manage Target Regions Files and Hotspot Files
• BED File Formats and Examples
• Download an Ion Reference File
• Details about the Ion hg19 Reference
• Manage DNA Barcodes and DNA Barcode Sets
• Update Reference Library Indexes
• Work with Test Fragments
• Work with Obsolete Reference Sequences

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