RNASeqAnalysis plugin configuration

The RNASeqAnalysis plugin can be configured with either the hg19 or mm10 reference genome when you plan a run. You can also add hg19 and mm10 annotation files.

This plugin requires the use of the RNA Seq Planned Run templates for sequencing runs: Ion RNA–Small or Ion RNA–Whole Transcriptome. If the RNA Seq Planned Run templates are not used when you run the plugin manually, you receive an error.

Setting

Description

Reference Genome

In the Configure Plugin dialog box, select:

  • hg19, or

  • mm10

Regenerate indices

Check to ensure that any pregenerated indexing and annotation files for the specified reference are deleted before the analysis starts. New files are generated as needed, which may add several hours to the plugin run time (approximately 3 hours for human-sized genomes).

Using this option is necessary if the plugin previously failed during (STAR) reference index generation of the reference sequence was updated.

To use the mouse mm10 Reference Genome with this plugin, first import the preloaded Ion reference genome using Torrent Suite™ Software. For more information, see Import a preloaded reference sequence file.

Related Topics
Parent topic: RNASeqAnalysis plugin