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interaction-track

README.md

Interaction Tracks

Interaction Tracks are tracks to display interacting genomic region pairs between different genomic windows. They are suitable for displaying paired interacting regions from experiments such as Hi-C and ChIA-PET.

Data Format

Currently GIVE supports importing interaction files with scripts into its data source.

Interaction data files are similar to BED files. They should be tab- or space-delimited text files. It should be noted that each row represents one part of interaction. Therefore, for binary interactions (as shown in Hi-C), every interaction will have two rows.

There are 6 fields for an interaction part:

chrom - The name of the chromosome.
chromStart - The starting position (0-based) of the entry in the chromosome.
chromEnd - The ending position of the entry in the chromosome. This base should not be included in the entry.
linkID - The unique ID for the interaction. All parts of the same interaction should have the same linkID. Because of this, the rows of the same interaction do not have to be adjacent to one another.
value - This value can be used to represent the strength of the interaction. Values will be shown in different colors. If no value is associated with any of the regions, use 1 for all of them. dirFlag - If the interaction is directional, this value can be used to indicate the directionality of this part. It should take a value of 0 or 1. NOTE: If the interaction is non-directional, this field should be omitted (use NULL) or filled by -1.

Display Modes

Currently interaction tracks can be displayed in one mode by setting the visibility property of the track:

  • Full - Interacting regions will be plotted between the view windows.
  • None - This track is not shown at all.

Supported Settings

The following settings of tracks are available for BED track:

  • track - The ID of the track. This value can be used in the default-track-id-list attribute in <chart-area> tags or <chart-controller> tags.
  • type - The type of the track. For BED tracks this should be bed.
  • shortLabel - The label that will be shown in the label region.
  • longLabel - More detailed description of the track. Will be shown in a future update.
  • priority - The order of the track in the browser. Smaller value means the the track will be shown in a higher location.
  • visibility - The display mode of the track. See Display Modes for details.
  • quantiles - The quantile values used for scaling. If color gradient based on quantile instead of absolute values is desired, an array of quantile values should be provided here. value will be scaled by quantiles before being mapped onto the color gradient.

Supported Metadata

Currently the tracks in GIVE can have properties used to store meta data of the track. The following meta data entries are used in filtering ENCODE tracks and will be expanded to support all tracks in a future update:

  • cellType - The name of the cell type. For ENCODE cell type names please refer to http://genome.ucsc.edu/ENCODE/cellTypes.html
  • labName - The name of the lab who contributed this data.
  • dataType - The type of the data, for example, 'Hi-C'.
  • trackFeature - Some data types require specification of additional features, for example, the antigen for the antibody in ChIA-PET experiments may need to be provided.