Table 1.
Method | Algorithm | Explored parameters | Tested values |
---|---|---|---|
groHMM | Hidden-Markov Model | -LtProbB (T): Log probability of the transcribed state to non-transcribed state | 50..500 |
UTS (σ2): variance in read counts of the non-transcribed state | 5..50 | ||
SICER | Clustering approach | windowSize: size of the windows to scan the genome width | 200..2000 |
gapSize: minimum gap size allowed between windows | 1x..10x | ||
HOMER | Transcription model | minBodySize: size of region for transcript body detection | 500..5000 |
bodyFold: fold enrichment for new transcript detection | 2..20 |