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Table 2 Optimal parameter values and error rates for each transcript-calling algorithm tested using GRO-seq data from MCF-7 cells

From: groHMM: a computational tool for identifying unannotated and cell type-specific transcription units from global run-on sequencing data

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