Method | Parameters | Optimal value | Number of transcripts | Median transcript length (bp) | Error | ||
---|---|---|---|---|---|---|---|
Merged annotation | Dissociated annotation | Rate | |||||
groHMM | -LtProbB (T) | 350 | 29,639 | 7,750 | 1,956 | 745 | 0.065 |
UTS (σ2) | 30 | ||||||
SICER | windowSize | 1,200 | 26,066 | 13,200 | 1,602 | 2,099 | 0.097 |
gapSize | 3,600 (3x) | ||||||
HOMER | minBodySize | 2,500 | 25,542 | 4,240 | 731 | 1029 | 0.047 |
bodyFold | 12 |