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