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.
- First feature - coordinates for the first feature and optional direction of interaction, separated by colons, commas or hyphens
- Second feature - coordinates for the second feature and optional direction of interaction, separated by colons, commas or hyphens
- 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.
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.
- Chromosome - chromosome of one feature in the interaction
- Start - start of one feature in the interaction
- End - end of one feature in the interaction
- Interaction - coordinates of the interacting feature and an optional score*
- ID - a unique ID for this feature
- 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.