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track type=interact name="interact Example One" description="An interact file" interactDirectional=true maxHeightPixels=200:100:50 visibility=full
browser position chr12:40,560,500-40,660,499
#chrom chromStart chromEnd name score value exp color sourceChrom sourceStart sourceEnd sourceName sourceStrand targetChrom targetStart targetEnd targetName targetStrand
chr12 40572709 40618813 rs7974522/LRRK2/muscleSkeletal 0 0.624 muscleSkeletal #7A67EE chr12 40572709 40572710 rs7974522 . chr12 40618812 40618813 LRRK2 +
chr12 40579899 40618813 rs17461492/LRRK2/muscleSkeletal 0 0.624 muscleSkeletal #7A67EE chr12 40579899 40579900 rs17461492 . chr12 40618812 40618813 LRRK2 +
chr12 40614433 40618813 rs76904798/LRRK2/nerveTibial 0 0.625 nerveTibial #FFD700 chr12 40614433 40614434 rs76904798 . chr12 40618812 40618813 LRRK2 +
chr12 40618812 40652520 rs2723264/LRRK2/lung 0 1.839 lung #9ACD32 chr12 40652519 40652520 rs2723264 . chr12 40618812 40618813 LRRK2 +
After the file loads in the Genome Browser, you should see four interactions displayed;
four variants interacting with the same gene (LRRK2).
Hovering the mouse over the curve peak of an interaction will display the interaction name
(SNP/gene/tissue).
Hovering over an interaction end will show the name of the end region (e.g. SNP or gene).
Clicking at one of the hoverable regions will show the details page for the interaction.
The interactDirectional setting causes reverse direction interactions (where
target precedes source) to be displayed as dashed lines. In this example, the green (lung)
interaction is in the reverse direction.
track type=interact name="interact Example Two" description="Chromatin interactions" useScore=on maxHeightPixels=200:100:50 visibility=full
browser position chr3:64,562,440-64,642,288
chr3 64496901 64584378 . 375 3 . 0 chr3 64496901 64498901 . . chr3 64581378 64584378 . .
chr3 64568052 64569134 . 400 3 . 0 chr20 52552477 52556062 . . chr3 64568052 64569134 . .
chr3 64596901 64615378 . 175 3 . 0 chr3 64596901 64600855 . . chr3 64612677 64615378 . .
chr3 64623042 64636663 . 800 4 . 0 chr3 64623042 64625153 . . chr3 64632961 64636663 . .
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After the file loads in the Genome Browser, you should see four interactions displayed on chromosome 3. Two of the interactions have both interacting regions in the browser view, and two have a single region. One of these interacts across chromosomes (with a region on chromosome 20), and the other with a region outside of the browser window (indicated by rectangular connector). The darkness of the interaction indicates the strength of the interaction. Also see the graphical representation of each column of this example data below.
In this example, you will create a bigInteract track out of an existing bigInteract format file, @@ -184,31 +184,31 @@
To create a custom track using this file:
track type=bigInteract interactUp=true name="interact Example Three" description="A bigInteract file" useScore=on visibility=full bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/interact/interactExample3.inter.bb
browser position chr3:63,820,967-63,880,091
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After the file loads in the Genome Browser, you should see a number of interactions, all arching as hills instead of valleys, with some curved and many rectangular indicating a connector to a region outside of the browser window. Press the 10x zoom out button to see the full connections.
In this example, you will use an example BED file to create a bigInteract file, allowing the data to be remotely accessed and exist within a track hub. The track settings for bigInteract on a hub can be viewed here.
This graphic represents the data in Example #2 with boxes around columns of data, separately illustrated as individual custom tracks in the lower image.
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The interact file format has 18 fields where the first 5 fields (box column1) are standard BED format fields, which define the span of the interaction to be viewed on a chromosome. In the below image, see the representation of box column1 and how it spans the length of each arc. Next, there are 3 fields for value, exp, and color before two sets of 5 fields that specify the coordinates, name, and strand of the source (box column2) and target (box column3) data, defining the endpoints of each interact arc. In the below image, the box column2 represents the left foot of each arc while the box column3 represents the right foot of each arc. The second row of the example data denotes an interaction to another chromosome, chr20, and thus is not represented by an arc.
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If you would like to share your interact/bigInteract data track with a colleague, learn how to create a URL by looking at Example 6 on this page.
Because bigInteract files are an extension of bigBed files, which are indexed binary files, it can be difficult to extract data from them. UCSC has developed the following programs to assist in working with bigBed formats, available from the binary utilities directory.
bigBedToBed — converts a bigBed file to ASCII BED format.