Table 2.

Number of detected transcripts by annotation classification reported by Cuffcompare and Cuffmerge

	Cuffcompare		Cuffmerge
Class Code	Transcripts, n	%	Transcripts, n	%
=	16,141	8.23	19,916	22.10
i	32,192	16.40	77	0.09
j	59,107	30.13	34,877	38.70
e	5,730	2.92	0	0.00
o	1,296	0.66	876	0.97
p	3,621	1.85	3	0.00
s	168	0.09	148	0.16
x	2,750	1.40	2,312	2.57
r	13,188	6.72	2	0.00
.	16,118	8.22	0	0.00
u	45,889	23.39	31,919	35.41
Total	196,200	100	90,130	100

=, Complete match of intron chain; i, a transfrag falling entirely within a reference intron; j, potentially novel isoform - at least 1 splice junction is shared with a reference transcript; e, single exon transfrag overlapping a reference exon and at least 10 bp of a reference intron, indicating a possible pre-mRNA fragment; o, generic exonic overlap with a reference transcript; p, possible polymerase run-on fragment (within 2 Kb of a reference transcript); s, an intron of the transfrag overlaps a reference intron on the opposite strand (likely due to read mapping errors); x, exonic overlap with reference on the opposite strand; r, repeat; “.”, multiple classifications; u, unknown intergenic transcript.