Difference between revisions of "Long-range"

Revision as of 23:08, 29 July 2018

Track file format for URL submitting

• The following format assumes you will compress and index the file at your own webserver, then use the URL of the file for submitting as custom track. The file upload function does require a different format which shown in next section.

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   .

Prepare track file

1. Compress and index this file:

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

2. Place 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.

Text file format for direct upload

You can directly upload long-range interaction data from a text file to the WashU Browser for display, without converting it into a track file.

Convert the 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.

In the coordinates, fields can be separated by colon, comma, and hyphen.

Unlike that is required for the long-range interaction track format, do not make duplicating records for each of the interacting pairs.

Go to the "File upload" app on the Browser to upload this file by choosing "pairwise interaction" as data type.