Table 1

Segtools analysis commands (segtools-...)

Command

Input

Output

Visualization


length-distribution

S

Segment length distribution by label

violin, bar plots (Figure 2)

nucleotide-frequency

S, G

Mono-/dinucleotide frequency by label

heat map (Figure IB)

signal-distribution

S, G

Signal mean and variance by label

heat map (Figure 3)

transition

S

Transition frequency between labels

heat map, graph diagram


aggregation

S, A

Label density around annotations

line plot (Figure 1A)

compare

S, S

Edit distances among all pairs of labels

heat map

overlap

S, A

Overlap of annotations by segments

PR curve, heat map


preprocess

A

An annotation in binary format

flatten

S, A

Segmentation with a label for every combination of labels in the input segmentations

feature-distance

S, A

Distance from each segment to nearest feature

html-report

S

HTML summary of Segtools command outputs


The commands offered by the Segtools package and their associated inputs and outputs. The first four commands analyze a single segmentation. The following three commands compare a segmentation to another segmentation or to an annotation. The last four commands generate no visualizations and are utilities to be used in conjunction with the other Segtools commands. In each row of the table, the second column indicates the input file types ("S" for segmentation, "A" for annotation, "G" for genomedata), and the fourth column indicates how the outputs are visualized (and a reference to an example figure in this article if one exists). "PR curve" refers to a precision-recall curve.

Buske et al. BMC Bioinformatics 2011 12:415   doi:10.1186/1471-2105-12-415

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