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 |