Skip to main content

Table 1 A part of CoolBox builtin tracks for visualizing different kinds of genomics data formats

From: CoolBox: a flexible toolkit for visual analysis of genomics data

Track type

File format

Description

XAxis

None

Coordinate of the reference genome

Spacer

None

For add vertical space between two tracks

BigWig

.bigwig

Track for bigWig file, draw the histogram

BedGraph

.bedgraph

Track for BedGraph file, draw the histogram

BAM

.bam

BAM track for visualize the coverage or alignment

BED

.bed

For visualization genome annotation, like refSeq genes and chromatin states

GTF

.gtf

Track of GTF file, for visualize gene annotation

Arcs

.pairs, .bedpe

Show the chromosome interactions get from ChIA-PET, HiChIP or Hi-C loop data

HiCMat

.cool, .mcool, .hic

Show the chromosome contact matrix from Hi-C data

Virtual4C

.cool, .mcool, .hic

Virtual 4C track, using Hi-C data to mimic 4C

DiScore

.cool, .mcool, .hic

Directional index of Hi-C matrix for detecting TAD

InsuScore

.cool, .mcool, .hic

Insulation score of Hi-C matrix for inferring TAD borders

HiCDiff

.cool, .mcool, .hic

Show the difference between two contact matrix

Selfish

.cool, .mcool, .hic

Apply the selfish algorithm [16] on two contact matrices to detect differential contact interactions

SNP

.tsv

Track for show SNPs Manhattan plot