RE: Could UCSC accept a .bedpe file

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Cath Tyner

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Feb 7, 2017, 8:13:56 PM2/7/17

to Yung-Chih Lai, UCSC Genome Browser Public Help Forum

Hello Gary,

Thanks for inquiring about file types which could support inter-chromosomal interactions. While we currently don't support the BEDPE file type, we have recently released a file type (called "longTabix") which supports inter & intra-chromosomal interactions by drawing an "arc" among paired regions in the UCSC Genome Browser.

Here is a paired-interaction track hub session that you can simply click on to load. Note the first track at the top of the display, you can click on any of the "arcs" or interaction connections to see details such as ID and score.

You can also change any of the associated tracks to "dense mode" or "full mode."

With the "longTabix" file type, you can create track hubs or custom tracks.

For example, here's an hg19 custom track that you can load:

First go to the UCSC Genome Browser > My Data > Custom Tracks
Next, paste the information below into the first box (with no line breaks) and then click "go" to see it in the browser.

track type="longTabix" name="longRange" bigDataUrl=http://hgwdev.cse.ucsc.edu/~braney/longRange/Esc_40kb_hindIII_rep1.over10.gz

In the browser, you can switch the track to "full mode" or "dense mode" and zoom out to see more interactions. As noted, you can click on any of the lines, or "arcs" to see details about that pair.

If you're interest

in creating a custom track or track hub, you can follow the steps below:

Note: Currently, only

the

indexed, binary "longTabix"

format

is supported, but a flat file format

for paired interactions

may be supported in the future.

To create the longTabix file:

1. Download tabix software from: http://samtools.sourceforge.net/tabix.shtml

2. Make a text file (must be tab delimited, with literal tabs) for your long-range interaction data with the following columns:

chromosome name
start coordinate
stop coordinate
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)
ID (unique non-negative integer)
relative direction of the interacting region

You will need to make

two

records for a pair of interacting loci, one record for each locus.

As an example, to represent interval "chr1:111-222" which interacts with interval "chr2:333-444" on a score of 55, you would use following two lines:

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 .

Again, note that the tabs must be literal, I have used "\t" to represent them in this example.

3. Compress the text file (you must use bgzip):

$ bgzip interaction.txt

Note: creates "interaction.txt.gz"

4. Build

the

tabix index of the compressed file:

$ tabix -p bed interaction.txt.gz

Note: The "interaction.txt.gz" is untouched but an index file "interaction.txt.gz.tbi" is generated. So, you now have two files (*.txt.gz and *.txt.gz.tbi).

5. You can now display this file as a custom long-range interaction track on the UCSC Genome Browser.
Place both files ".gz" and ".gz.tbi"

the

same

Yung-Chih Lai

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Feb 8, 2017, 10:28:25 AM2/8/17

to Cath Tyner, UCSC Genome Browser Public Help Forum

Hi Cath,

Thank you so much for your information.

Best,

Gary

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