Preferred transcripts in default analysis workflows

The default analysis workflows that are provided in Ion Reporter™ Software include an annotations set with a preferred transcript set, the RefGene canonical transcripts. The default annotation set that includes the default RefSeq canonical transcripts is named All.

Default analysis workflows that use the All annotation set report only transcripts that are included in the RefGene canonical transcripts. By default, the following RefGene canonical transcripts are included in the All annotation set:

• RefGene

• Functional

• Canonical

• Transcript Scores

All other transcripts are filtered out and not reported.

To instead have additional transcripts reported in your analyses, see Create annotation set without preferred transcript sets.