Friday, March 7, 2014

v33 (1 of 2): upload long-range interaction data

From version 33 you can now upload long-range interaction data in the form of text files. This is very suitable for showing small quantity of data (including but not restricted to 5C, ChIA-PET, Hi-C results), and you don't need to go through trouble of converting your data into the required format and host it as a custom track.

To start, convert your data into a simple format like this:

chr1,713605,715737     chr1,720589,722848 2
chr1,717172,720090 chr1:761197-762811 2
chr1,755977,758438 chr1:758539-760203 2

Each line indicates an interaction event involving two regions from the genome. 3 fields are present for each line: coordinate of region 1, coordinate of region 2, score.

  • For the coordinates, you can use a non-word character to separate fields, but don't use tab.
  • The score is optional.
  • Unlike that is required for the long-range interaction track format, do not make duplicating records for each of the interacting pairs.

Go to Apps > File upload:

Upload your file. At the "Edit" panel, choose "Pairwise interaction" option and click "Add" button. The track will be loaded: