f4ace97438e173daf68c76153a4481de73879798 jcasper Fri Nov 8 16:46:02 2019 -0800 Initial commit of supporting docs for hic track type, refs #22316 diff --git src/hg/htdocs/goldenPath/help/hgHicTrackHelp.html src/hg/htdocs/goldenPath/help/hgHicTrackHelp.html new file mode 100755 index 0000000..c626f78 --- /dev/null +++ src/hg/htdocs/goldenPath/help/hgHicTrackHelp.html @@ -0,0 +1,96 @@ +<!DOCTYPE html> +<!--#set var="TITLE" value="Genome Browser hic Tracks" --> +<!--#set var="ROOT" value="../.." --> + +<!-- Relative paths to support mirror sites with non-standard GB docs install --> +<!--#include virtual="$ROOT/inc/gbPageStart.html" --> + +<!-- hic Track Help Page --> + +<h1>Configuring hic tracks</h1> +<p> +Genome Browser hic tracks display heatmaps of chromatin folding data, and may be configured +in several ways to highlight different aspects of the data. By default, hic tracks will use +auto-scale options for resolution and score coloring. +</p> +<p> +The following section describes configuration settings available to hic tracks. For more information +on setting up and uploading hic data, click the link on <a href="hic.html" target="_blank"> +hic custom track creation</a>. +</p> +<h2>Configuring the display mode</h2> +<p> +There are three display methods available for Hi-C heatmaps: square, triangle, and arc. +<p class='text-center'> + <img src="../../images/hicDrawModes.png" alt="hic draw modes"> +</p> +<p> +Square mode provides a traditional Hi-C display in which chromosome positions are mapped along the +top-left-to-bottom-right diagonal, and interaction values are plotted on both sides of that diagonal +to form a square. The upper-left corner of the square corresponds to the left-most position of the +window in view, while the bottom-right corner corresponds to the right-most position of the window. +</p><p> +The color shade at any point within the square shows the proximity score for two genomic regions: +the region where a vertical line drawn from that point intersects with the diagonal, and the region +where a horizontal line from that point intersects with the diagonal. A point directly on the +diagonal shows the score for how proximal a region is to itself (scores on the diagonal are usually +quite high unless no data are available). A point at the extreme bottom left of the square shows the +score for how proximal the left-most position within the window is to the right-most position within +the window. +</p><p> +In triangle mode, the display is quite similar to square except that only the top half of the square +is drawn (eliminating the redundancy), and the image is rotated so that the diagonal of the square +now lies on the horizontal axis. This display consumes less vertical space in the image, although it +may be more difficult to ascertain exactly which positions correspond to a point within the +triangle. +</p><p> +In arc mode, simple arcs are drawn between the centers of interacting regions. The color of each arc +corresponds to the proximity score. Self-interactions are not displayed. +</p> +<p> +<strong>Score normalization settings</strong> +</p><p> +Score values for this type of display correspond to how close two genomic regions are in 3D space. A +high score indicates more links were formed between them in the experiment, which suggests that the +regions are near to each other. A low score suggests that the regions are farther apart. High scores +are displayed with a more intense color value; low scores are displayed in paler shades. +</p><p> +There are four score values available in this display: NONE, VC, VC_SQRT, and KR. NONE provides raw, +un-normalized counts for the number of interactions between regions. VC, or Vanilla Coverage, +normalization (Lieberman-Aiden <em>et al</em>., 2009) and the VC_SQRT variant normalize these count +values based on the overall count values for each of the two interacting regions. Knight-Ruiz, or +KR, matrix balancing (Knight and Ruiz, 2013) provides an alternative normalization method where the +row and column sums of the contact matrix equal 1. +</p><p> +Color intensity in the heatmap goes up to indicate higher scores, but eventually saturates at a +maximum beyond which all scores share the same color intensity. The value of this maximum score for +saturation can be set manually by un-checking the "Auto-scale" box. When the +"Auto-scale" box is checked, it automatically sets the saturation maximum to be double +(2x) the median score in the current display window. +</p><p> +<strong>Resolution settings</strong> +</p><p> +The resolution for each track is measured in base pairs and represents the size of the bins into +which proximity data are gathered. The list of available resolutions ranges from 1kb to 10Mb. There +is also an "Auto" setting, which attempts to use the coarsest resolution that still +displays at least 500 bins in the current window. +</p> +<p> +When you have finished making your configuration changes, click the <button>Submit</button> button +to return to the annotation track display page.</p> +<h2>References</h2> +<p> +Knight P, Ruiz D. +<a href="https://doi.org/10.1093/imanum/drs019" target="_blank"> +A fast algorithm for matrix balancing</a>. +<em>IMA J Numer Anal</em>. 2013 Jul;33(3):1029-1047. +</p><p> +Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, +Sabo PJ, Dorschner MO <em>et al</em>. +<a href="http://www.sciencemag.org/cgi/pmidlookup?view=long&pmid=19815776" target="_blank"> +Comprehensive mapping of long-range interactions reveals folding principles of the human genome</a>. +<em>Science</em>. 2009 Oct 9;326(5950):289-93. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/19815776" target="_blank">19815776</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2858594/" target="_blank">PMC2858594</a> + +<!--#include virtual="$ROOT/inc/gbPageEnd.html" -->