eeb045a2a436539a1a8797984dfe7dfcaacf789d brianlee Wed Sep 11 17:09:15 2019 -0700 Putting ASHG poster information into the interact.html help page diff --git src/hg/htdocs/goldenPath/help/interact.html src/hg/htdocs/goldenPath/help/interact.html index c21a9dd..318db40 100755 --- src/hg/htdocs/goldenPath/help/interact.html +++ src/hg/htdocs/goldenPath/help/interact.html @@ -60,31 +60,32 @@ string sourceName; "Identifier of source/lower/this region" string sourceStrand; "Orientation of source/lower/this region: + or -. Use . if not applicable" string targetChrom; "Chromosome of target region (directional) or upper region. For non-directional interchromosomal, chrom of other region" uint targetStart; "Start position in chromosome of target/upper/this region" uint targetEnd; "End position in chromosome of target/upper/this region" string targetName; "Identifier of target/upper/this region" string targetStrand; "Orientation of target/upper/this region: + or -. Use . if not applicable" ) </code></pre> <a name="columnDefinition"></a> <h6>Column Explanations</h6> <p> The first 5 fields of the interact format are the same as the first 5 fields of the standard -<a href="../../FAQ/FAQformat#format1">BED</a> format. +<a href="../../FAQ/FAQformat#format1">BED</a> format. See a graphical depiction +<a href="#understanding">below</a> of the columns. </p> <p> When creating bigInteract files, we encourage you to customize the title and field descriptions of the prototype autoSql schema to better describe your data. Customizing this file will make your data more easily interpreted by users, who will see the field descriptions when accessing the track data from the Table Browser, when viewing items on the Genome Browser details pages (via the "view table schema" link), and (for users who download files), from the -as option of the bigBedInfo tool.</p> <p> As an example, if the dataset represents SNP/gene interactions, replace 'sourceName' and related fields with 'snpName', etc, and 'targetName' and related fields with 'geneName', etc., editing the field descriptions to reflect the changes you make. For non-directional data such as ChIA-PET, one could use 'region1' and 'region2'.</p> @@ -155,31 +156,32 @@ chr3 64623042 64636663 . 800 4 . 0 chr3 64623042 64625153 . . chr3 64632961 64636663 . . </code></pre></li> <li>Click the "submit" button.</li> </ol> </p> <ol> <img width="1080" height="148" src="../../images/interactExample2.png"> </ol> <p> 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. +The darkness of the interaction indicates the strength of the interaction. Also see the graphical +representation of each column of this example data <a href="#understanding">below</a>. </p> <a name="example3"></a> <h6>Example #3</h6> <p> In this example, you will create a bigInteract track out of an existing bigInteract format file, located on the UCSC Genome Browser http server. This file contains data for the hg19 assembly. This example also contains the <a href="./trackDb/trackDbHub.html#interactUp" target="_blank"><code>interactUp=true</code></a> setting to flip the arcs of the interact display.</p> </p> <p> To create a custom track using this file: <ol> <li>Construct a track line referencing the file and set the browser position to show region @@ -239,47 +241,66 @@ <li>To fully take advantage of creating a bigInteract file, create a <a href="hgTrackHubHelp.html">Track Hub</a> and use a stanza such as the following: <pre><code> track exampleInteractTrack type bigInteract visibility full shortLabel exInteract longLabel Example interact track spectrum on scoreMin 175 maxHeightPixels 300:150:20 bigDataUrl interactExample4.inter.bb </code></pre> </ol> +<a name="understanding"></a> +<h2>Understanding the interact file format</h2> +<p> +This graphic represents the data in <a href="#example2">Example #2</a> with boxes around +columns of data, separately illustrated as individual custom tracks in the lower image.</p> +<img width="1170" height="88" src="../../images/interactUnderstanding1.png"> +<p> +The interact file format has <a href="#interact">18 fields</a> where the <b>first 5 fields</b> +<b style="color:#993399;">(column 1 box)</b> are standard <a href="../../FAQ/FAQformat#format1">BED</a> +format fields, which <b>define the span</b> of the interaction to be viewed on a chromosome. In the +below image see the representation of column 1 and how it spans the length of each arc. Next, there +are 3 fields for value, exp, and color before <b>two sets of 5 fields</b> that specify +the coordinates, name, and strand of the <b>source</b> <b style="color:#336600;">(column 2 box)</b> +and <b>target</b> <b style="color:#FF3333;">(column 3 box)</b> data, defining the endpoints of +each interact arc. In the below image the column 2 box represents the left foot of each arc +while the column 3 box 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.</p> +<img width="1170" height="237" src="../../images/interactUnderstanding2.png"> + <h2>Sharing your data with others</h2> <p> 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 <a href="customTrack.html#EXAMPLE6">this page</a>.</p> <h2>Extracting data from the bigInteract format</h2> <p> 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 <a href="http://hgdownload.soe.ucsc.edu/admin/exe/">binary utilities directory</a>.</p> <ul> <li> <code>bigBedToBed</code> — converts a bigBed file to ASCII BED format.</li> <li> <code>bigBedSummary</code> — extracts summary information from a bigBed file.</li> <li> <code>bigBedInfo</code> — prints out information about a bigBed file. Use the -as option to see the file field descriptions.</li> </ul> <p> -As with all UCSC Genome Browser programs, simply type the program name (with no parameters) at the +As with all UCSC Genome Browser programs, one can type the program name (with no parameters) at the command line to view the usage statement.</p> <h2>Troubleshooting</h2> <p> If you encounter an error when you run the <code>bedToBigBed</code> program, check your input file for data coordinates that extend past the end of the chromosome. If these are present, run the <code>bedClip</code> program (<a href="http://hgdownload.soe.ucsc.edu/admin/exe/">available here</a>) to remove the problematic row(s) in your input file before running the <code>bedToBigBed</code> program.</p> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->