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 indexing and annotation files previously generated 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 reference index
generation or 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.
