Table 1.

An example of transcript response profile (TRP) matrix for tx1 based on simulated sample1

Eqclass	tx1	tx2	tx3	tx4	tx5
eqclass1	20	20	0	20	20
eqclass2	850	850	850	0	0
eqclass3	130	0	0	130	0
Sum	1000	870	850	150	20

Note: In this sample1 we set only tx1 expressed and we use Rapmap for read mapping. Next we summarize the read alignment results into the TRP matrix. The exon-sharing is presented by equivalence class (eqclass) as the rows in the matrix. Transcript tx5 is filtered out because it fails the false positive threshold of H = 2.5%.