be3e19cef95c229660435527393d852a81da80d2 brianlee Wed Jun 12 14:18:12 2019 -0700 Fixing a maxPixel reference Bob and I noticed in the interact help page. diff --git src/hg/htdocs/goldenPath/help/interact.html src/hg/htdocs/goldenPath/help/interact.html index 80af8f6..c21a9dd 100755 --- src/hg/htdocs/goldenPath/help/interact.html +++ src/hg/htdocs/goldenPath/help/interact.html @@ -94,31 +94,31 @@ BED or other format file to display the source and target region labels.

Creating interact and bigInteract custom tracks

Example #1

In this example, you will create an interact custom track using example SNP/gene interaction data in multiple tissues. This example uses the interaction coloring and directionality features of the interact track type.

  1. Paste the following track line into the custom track management page for the human assembly hg19.
    
    -track type=interact name="interact Example One" description="An interact file" interactDirectional=true maxHeightPixels=50:100:200 visibility=full
    +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   +
        
  2. Click the "submit" button.

@@ -135,31 +135,31 @@

Example #2

In this example, you will create an interact custom track using example chromatin interaction data. This type of data is non-directional and commonly would represent a single experiment, with the interaction score being of interest. The settings below display using the gray-scale coloring feature, where the darkness of the interaction is based on the score.

  1. Paste the following track line into the custom track management page for the human assembly hg19.
    
    -track type=interact name="interact Example Two" description="Chromatin interactions" useScore=on maxHeightPixels=50:100:200 visibility=full
    +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        .       .
        
  2. Click the "submit" button.

After the file loads in the Genome Browser, you should see four interactions displayed on