Commit e72444b1 authored by Michael Menzel's avatar Michael Menzel

Added tutorial and changed sample bed file

parent 813003c1
......@@ -117,6 +117,12 @@ public class ApplicationController implements ErrorController {
return "faq";
}
@RequestMapping("/tutorial")
public String tutorial() {
return "tutorial";
}
@RequestMapping("/contact")
public String contact(){
......
......@@ -50,10 +50,10 @@ public class SampleController {
if(System.getenv("HOME").contains("menzel")) {
String path = "/home/menzel/Desktop/THM/lfba/enhort";
samplefilepath = path+"/HIV-hg19.bed";
samplefilepath = path + "/sites.hiv.all.wu_03.tab";
} else {
String path = "/home/mmnz21/enhort";
samplefilepath = path+"/HIV-hg19.bed";
samplefilepath = path + "/sites.hiv.all.wu_03.tab";
}
if (!new File(samplefilepath).exists()) {
......@@ -72,7 +72,7 @@ public class SampleController {
currentSession.setOriginalFilename("HIV");
BackendCommand backendCommand = //new BackendCommand(userSites, Command.Task.ANALZYE_SINGLE);
new BackendCommand.Builder(Command.Task.ANALZYE_SINGLE, userSites.getAssembly()).sites(userSites).build();
new BackendCommand.Builder(Command.Task.ANALZYE_SINGLE, userSites.getAssembly()).sites(userSites).minBg(userSites.getPositionCount()).build();
try {
/////////// Run analysis ////////////
......
......@@ -18,3 +18,10 @@ p {
#faqlogo {
width: inherit;
}
.tutorialimage {
width: 700px;
border: 1px solid black;
margin-top: 30px;
margin-bottom: 30px;
}
\ No newline at end of file
......@@ -34,8 +34,7 @@
Analysis</a>. Enhort then tests your genomic positions against a set of annotations.
Using the Guided Analysis you can select annotations, based on your assembly number and cellline, see
the section about the Guided Analysis usage below on this page. The quickstart upload uses a curated
list of annotations, containing genes and gene related features, genotoxicity, accessibility and a
selection of histone modifications.
list of annotations, containing genes and gene related features to test your sites against.
</p>
<p>
......@@ -52,7 +51,8 @@
</p>
<p>
If you are interested in seeing some results use the <a href="/sample">sample data link</a>.
If you are interested in seeing some results use the <a href="/sample">sample data link</a>. A more
comprehensive tutorial is available <a href="/tutorial">here</a>.
</p>
<h3>Guided Analysis</h3>
......
<!DOCTYPE html SYSTEM "http://www.thymeleaf.org/dtd/xhtml1-strict-thymeleaf-spring4-4.dtd">
<html xmlns:th="http://www.thymeleaf.org"
xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="UTF-8"/>
<title>Enhort - Genomic Position Profiling - Tutorial</title>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8"/>
<link rel="stylesheet" media="screen" href="../static/css/bootstrap.min.css" th:href="@{/css/bootstrap.min.css}"/>
<link rel="stylesheet" media="screen" href="../static/css/faq.css" th:href="@{/css/faq.css}"/>
<script src="/js/jquery-1.12.0.min.js" th:href="@{/js/jquery-1.12.0.min.js}"></script>
<script src="/js/bootstrap.min.js" th:href="@{/js/bootstrap.min.js}"></script>
</head>
<body>
<div th:include="header:: bar"></div>
<div class="container">
<div class="main col-10">
<img src="title_logo.png" id="faqlogo"/>
<h2>Tutorial</h2>
<p>
In this short tutorial a set of 1141475 HIV integration sites are analysed using Enhort.
</p>
<h4>Upload integration sites</h4>
<hr/>
<p>
At first, integration sites have to uploaded in a .bed-file. In this example set of about 1m HIV integration
sites taken from the
<a href="https://rid.ncifcrf.gov/">Retrovirus Integration Database</a> is used. The wizard is selected on
the main page:
</p>
<img src="img/tutorial/tut1.png" class="tutorialimage"/>
<p>
And on the following page the .bed-file is selected on the local computer.
</p>
<h4>Select annotations</h4>
<hr/>
The sites are then uploaded and the overview for available annotations is shown:
<img src="img/tutorial/tut2.png" class="tutorialimage"/>
<p>
Single annotations can be selected by clicking on the blue squares. A set of annotations for a cell line or
all annotations in a column
can be selected by clicking on the row or column header. For example, all cell line independent annotations
are selected in the following example, as well as
annotations for HeLa:
</p>
<img src="img/tutorial/tut3.png" class="tutorialimage"/>
<h4>Review results and add a covariate</h4>
<hr/>
<p>
The results for the given sites and selected covariates are then displayed in a table, containing the effect
size and p value of each annotation, as well
as overview over the annotation groups. Each row can be expanded to get exact integration counts for each
annotation:
</p>
<img src="img/tutorial/tut4.png" class="tutorialimage"/>
<p>
From here the user can select covariates to alter the integation preference
of the background control sites. For example, HIV is known to integrate near genes which is observable in
the upper image. The annotation track RefSeq genes can
be selected as covariate to adapt the background for this known preference. To do this the marked checkbox
is selected and with the button 'Run again' the
background is changed. In the following image we see RefSeq genes was added to list of covariate on the
right and now has the exact same integration preference as the HIV sites:
</p>
<img src="img/tutorial/tut5.png" class="tutorialimage"/>
<p>
This adaptation then changes the significance and fold change of several annotations tracks in the main
table. In the following the complete table of selected annotations is shown
with 'houskeeping genes' expanded to show exact integration counts:
</p>
<img src="img/tutorial/tut6.png" class="tutorialimage"/>
<h4>Further possibilites</h4>
<hr/>
<p>
In the upper part different tabs are located containing further analysis of the given sites, as well as the
option to download the background sites or results.
Depending on the individual scientific question other covariates can be selected to build a specialized
background model.
</p>
</div>
</div>
</body>
</html>
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