Long-range

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Make a text file for your long-range interaction data with following columns:

  1. chromosome name
  2. start coordinate
  3. stop coordinate
  4. information about the interacting region (e.g. chrX:123-456,3.14, where "chrX:123-456" is the coordinate of the mate, and "3.14" is the score of the interaction)
  5. ID (unique non-negative integer)
  6. relative direction of the interacting region

Be sure to make TWO records for a pair of interacting loci, one record for each locus.

As an example, interval "chr1:111-222" interacts with interval "chr2:333-444" on a score of 55, we will use following two lines to represent this interaction:

chr1   \t   111   \t   222   \t   chr2:333-444,55   \t   1   \t   .
chr2   \t   333   \t   444   \t   chr1:111-222,55   \t   2   \t   .

Compress and index this file:

bgzip interaction.txt
tabix -p bed interaction.txt.gz

Put the two files "interaction.txt.gz" and "interaction.txt.gz.tbi" on a web server. Two files must be in the same directory. Obtain the URL for file "interaction.txt.gz" for displaying on the Browser.