Transcript assembly and annotations: Bias and adjustment
Fig 9
An illustrative example for the three criteria used to define transcripts with intron retentions.
Identical boundaries are marked with vertical dashed lines. Transcript t2 satisfies criterion 1 (it has lower abundance than t1, and its first exon spans the second intron of t1). Transcript t3 satisfies criterion 2 (it has lower abundance than t1 and its last exon spans the fourth intron of t1). Transcript t4 satisfies criterion 3 (it has lower abundance than t1 and its second exon fully covers the second intron of t1).