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Pairwise Interactions File Formats - Definition and supported options

Ensembl supports the two formats established by WashU for long-range pairwise interactions, as follows:

Simple text format

This consists of one interaction per line, with three fields separated by spaces or tabs.

  1. First feature - coordinates for the first feature and optional direction of interaction, separated by colons, commas or hyphens
  2. Second feature - coordinates for the second feature and optional direction of interaction, separated by colons, commas or hyphens
  3. Score - score for the interaction, or an RGB value (expressed as a comma-separated string e.g. 0,255,0)
chr1,713605,715737,-     chr1,720589,722848,-      2
chr1,717172,720090,+     chr1:761197-762811,+      2
chr1,755977,758438,-     chr1:758539-760203,-      2

Data in this format can be uploaded to our website either by pasting into the Add Track form, or uploading a file (default extension is .txt) - select 'Pairwise interaction' as the format.

Tabix-indexed format

This is a tab-separated format with more detail, and has one feature per line. Note that there must be two lines per interaction, one for each feature.

  1. Chromosome - chromosome of one feature in the interaction
  2. Start - start of one feature in the interaction
  3. End - end of one feature in the interaction
  4. Interaction - coordinates of the interacting feature and an optional score*
  5. ID - a unique ID for this feature
  6. Direction - relative direction of the interaction

* As with the simple format, the score can be an RGB value expressed as a comma-separated string (e.g. 0,255,0).

chr1    111   222   chr1:333-444,255,0,0   1   +
chr1    222   333   chr1:444-555,0,0,255   2   -
chr1    333   444   chr1:111-222,255,0,0   3   +
chr1    444   555   chr1:222-333,0,0,255   4   -

Data in this format must be attached to Ensembl via a URL - select 'Pairwise interactions (indexed) on the 'Add track' form.

More information about both these formats can be found on the wubrowse wiki.