% my $url_root = $m->comp("SELF:url_root");

<h1>Tutorials</h1>

<p>The tutorials serve as a walkthrough through Circos. Each <a
href="<% $url_root %>/tutorials/lessons">lesson</a> presents a
specific feature of Circos. 

<h2>Creating a Tutorial Image</h2>

<p>Once you <a href="<% $url_root %>/software/download">download and install</a> Circos, try creating images for some lessons to see how Circos works.

<pre>
<span class=comment># install circos</span>
&gt; tar xvfz circos-x.xx.tgz
&gt; cd circos-x.xx
&gt; cd tutorials/2/2
<span class=comment># now try tutorial 2.2</span>
&gt; ../../../bin/circos -conf ./circos.conf
</pre>

<p>In each tutorial directory (e.g. <code>tutorials/2/2</code>), there will be several configuration files (<code>*.conf</code>). There will always be a <code>circos.conf</code> file &mdash; this is the central configuration file that you pass to the Circos binary with the <code>-conf</code> flag. There may be other variants of the central configuration file (e.g. <code>circos-2.conf</code>) &mdash; these illustrate other aspects of the features discussed in the tutorial.

<h2>Creating Your Own Image</h2>

<p>The first thing you will need is the karyotype for your genome. The karyotype defines the chromosomes (name, size, color) and, optionally, the cytogenetic band pattern. You can obtain karyotypes for many genomes from the <code>cytoBandIdeo</code> table (UCSC genome browser).

<p>You can download the karyotype from the <a href="http://genome.ucsc.edu/cgi-bin/hgTables">table browser</a> or directly for

human 
<a href="http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/cytoBandIdeo.txt.gz">hg19 (Feb 2009)</a>
<a href="http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/cytoBandIdeo.txt.gz">hg18 (Mar 2006)</a>,
mouse
<a href="http://hgdownload.cse.ucsc.edu/goldenPath/mm9/database/cytoBandIdeo.txt.gz">mm9 (Jul 2009)</a>
<a href="http://hgdownload.cse.ucsc.edu/goldenPath/mm8/database/cytoBandIdeo.txt.gz">mm8 (Mar 2006)</a>,
rat
<a href="http://hgdownload.cse.ucsc.edu/goldenPath/rn4/database/cytoBandIdeo.txt.gz">rn4 (Nov 2004)</a>
<a href="http://hgdownload.cse.ucsc.edu/goldenPath/rn4/database/cytoBandIdeo.txt.gz">rn3 (Jun 2003)</a>,
or <a href="http://hgdownload.cse.ucsc.edu/downloads.html">other species</a>. 

<p>Once you have decided which <a href="<% $url_root %>/tutorials/lessons/ideograms">ideograms</a> to draw (ideograms are the graphical representation of chromosomes), add <a href="<% $url_root %>/tutorials/lessons/highlights">highlights</a>, <a href="<% $url_root %>/tutorials/lessons/2d_tracks">2D tracks</a> and <a href="<% $url_root %>/tutorials/lessons/links">links</a>.</p>

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