<commit_before>{% extends "_layouts/default.html" %} {% block custom_head %}
<style>
#checkout.affix {
    position: fixed;
    top: 20px;
    width: 136px;
}
</style>
{% endblock %} 


{% block content %}
<div class="row">
    <div class="col-md-12">
        <div class="row">

        <div class="col-md-4">
            <h3>Alignment Data</h3>
            <p>We aligned all wild isolate genomes to the WS245 version of the N2 genome. These data are stored using the <abbr data-toggle="tooltip" data-placement="bottom" title="Binary sequence Alignment/Map format">BAM</abbr> and <abbr data-toggle="tooltip" data-placement="bottom" title="Compressed sequence Alignment/Map format">CRAM</abbr> formats. <abbr data-toggle="tooltip" data-placement="bottom" title="Compressed sequence Alignment/Map format">CRAM</abbr> files are substantially smaller than <abbr data-toggle="tooltip" data-placement="bottom" title="Binary sequence Alignment/Map format">BAM</abbr> files.</p>

            <p><a href="http://biobits.org/samtools_primer.html"  target="_blank">Learn about alignment data here</a>.</p>

            <p>CRAM files are substantially smaller than BAM files, but require the reference to be converted to BAM files. We are currently using WS245 (<strong><a href="https://northwestern.box.com/shared/static/ijlhhd1hwlbr5vvasjg35yjux1p5n01g.gz">Download</a></strong>).

        <h4>Downloading All Alignment Data</h4>
            <p>Interested in downloading everything? Use the scripts below! Before these scripts will work, you need to download and install <strong>wget</strong>. We recommend using <a href="http://brew.sh">Homebrew</a> for this installation (Unix/Mac OS), or <a href="https://www.cygwin.com/">Cygwin</a> on windows. See the <a href="{{ url_for("help_item",filename="FAQ")}}">FAQ</a> for details on installing <strong>wget</strong>. </p>
            <ul>
                <li><a href="{{ url_for("download_script", filetype="bam") }}">Download BAMs</a></li>
                <li><a href="{{ url_for("download_script", filetype="cram") }}">Download CRAMs</a></li>
            </ul>
            </p>

        </div>


        <div class="col-md-4">
            <h3>Variant Data</h3>
            <p>We used samtools to identify single-nucleotide variant  (SNV) sites as compared to the N2 reference genome (WS245). Variant data are provided as <abbr data-toggle="tooltip" data-placement="bottom" title="Variant Caller Format">VCF</abbr> or tab-delimited files.</p>

            <p><a href="http://biobits.org/samtools_primer.html#UnderstandingtheVCFFormat" >Learn more about VCF files here</a>.</p>

            <h4>VCF</h4>
            <p>The file below is a single <abbr data-toggle="tooltip" data-placement="bottom" title="Variant Caller Format">VCF</abbr> containing SNVs for all wild isolates.</p>
            <p><a href="https://storage.googleapis.com/andersen_dist/vcf/all/{{ build }}/WI.{{ build }}.snpeff.vcf.gz"><img src="{{ url_for('static',filename = 'img/icons/vcf.png')}}" style="width: 50px; margin-right:20px; margin-bottom:10px;" class="pull-left"></a>
            <strong style="line-height:50px;"><a href="https://storage.googleapis.com/andersen_dist/vcf/all/{{ build }}/WI.{{ build }}.snpeff.vcf.gz">WI.{{ build }}.snpeff.vcf.gz</a></strong></p>

            <div style = "clear:both;"></div>
          
            <p>You can also access specific regions of <abbr data-toggle="tooltip" data-placement="bottom" title="Variant Caller Format">VCF</abbr> files (rather then the entire file) from the command line: <button type="button" class="btn btn-primary btn-xs" data-toggle="modal" data-target="#cli_example">
              See Example
            </button></p>

            <h4>Methods</h4>
            <p>Information regarding alignment, variant calling, and annotation are available <a href="{{ url_for('help_item', filename = "Methods") }}">here</a>.

        </div>
        </br>
        <div class="col-md-4">
                 <div class="panel panel-default">
                        <div class="panel-heading">Strain Data</div>
                        <div class="panel-body">
                            Strain Data including isolation location, isotype information, and more is available for download.<br /><br />
                            <a href="{{ url_for('strain_metadata') }}" type="button" class="btn btn-default btn-block btn-success">Download Strain Data</a>
                        </div>
                    </div>

            <h4>Included Variants</h4>
            <p>Currently, we have performed variant calling across all wild isolates. We are working to add additional variant classes including insertion/deletion, structural, transposon, and additional variant classes.</p>
            <h4>Transposon Data</h4>
            <p>We have recently performed an anaysis characterizing Transposon variation in <em>C. elegans</em>. The dataset will be further integrated with the site resources as time goes on. For now, the raw data are available below.</p>
            <a href="https://storage.googleapis.com/andersenlab.org/publications/2017Laricchia/tes_cender.bed" type="button" class="btn btn-default btn-block btn-success">Download Transposon Data</a>
        </div>
        </div>
        <hr />
        <input id="filter" type="text" class="form-control pull-right" style = "width:200px;" placeholder="Enter Strain Name" action="#">
        <table class="table table-hover table-striped">
            <thead>
                <tr>
                        <th style="width: 200px;">
                            <span class="tooltip-item" data-toggle="tooltip"  data-placement="bottom" title="Name of strain we distribute as a representative of an isotype.">
                            Reference Strain
                            </span>
                        </th>
                        <th style="width: 200px;">
                            <span class="tooltip-item" data-toggle="tooltip"  data-placement="bottom" title="Name assigned to a group of strains that share the same genome-wide haplotype.">
                            Isotype
                            </span>
                        </th>
                        <th style="width: 200px;">
                        <span class="tooltip-item" data-toggle="tooltip"  data-placement="bottom" title="Individually isolated strains; If strains are assigned to the same isotype they are > 99.93% genetically identical">
                        Strains
                        </span></th>
                    </th>
                    <th style="width: 200px;">BAM</th>
                    <th style="width: 200px;">CRAM</th>
                    <th>Tab-delimited variants</th>
                </tr>
            </thead>
            <div style="height: 30px;" ></div>
            <tbody class="searchable">
                {% for isotype, strains in strain_listing|groupby('isotype') %}
                <tr>
                        <td>
                            {% for s in strains %}
                                {% if s.reference_strain %}
                                    <strong>
                                    {{ s }}
                                    </strong>
                                {% endif %}
                            {% endfor %}
                        </td>

                    <td><a href="{{ url_for('isotype_page', isotype_name=isotype) }}">{{ isotype }}</a></td>
                    <td>{% for s in strains %}
                                {{ s }}
                        {% endfor %}
                    </td>
                    <td>
                        {% if strains[0].bam_file %}
                            <a href="{{ strains[0].bam_file }}">{{ isotype }}.bam</a>
                            <strong>/</strong> <a href="{{ strains[0].bam_index }}">.bai</a> 
                        {% endif %}
                    </td>
                    <td><commit_msg>Add # to data page<commit_after>{% extends "_layouts/default.html" %} {% block custom_head %}
<style>
#checkout.affix {
    position: fixed;
    top: 20px;
    width: 136px;
}
</style>
{% endblock %} 


{% block content %}
<div class="row">
    <div class="col-md-12">
        <div class="row">

        <div class="col-md-4">
            <h3>Alignment Data</h3>
            <p>We aligned all wild isolate genomes to the WS245 version of the N2 genome. These data are stored using the <abbr data-toggle="tooltip" data-placement="bottom" title="Binary sequence Alignment/Map format">BAM</abbr> and <abbr data-toggle="tooltip" data-placement="bottom" title="Compressed sequence Alignment/Map format">CRAM</abbr> formats. <abbr data-toggle="tooltip" data-placement="bottom" title="Compressed sequence Alignment/Map format">CRAM</abbr> files are substantially smaller than <abbr data-toggle="tooltip" data-placement="bottom" title="Binary sequence Alignment/Map format">BAM</abbr> files.</p>

            <p><a href="http://biobits.org/samtools_primer.html"  target="_blank">Learn about alignment data here</a>.</p>

            <p>CRAM files are substantially smaller than BAM files, but require the reference to be converted to BAM files. We are currently using WS245 (<strong><a href="https://northwestern.box.com/shared/static/ijlhhd1hwlbr5vvasjg35yjux1p5n01g.gz">Download</a></strong>).

        <h4>Downloading All Alignment Data</h4>
            <p>Interested in downloading everything? Use the scripts below! Before these scripts will work, you need to download and install <strong>wget</strong>. We recommend using <a href="http://brew.sh">Homebrew</a> for this installation (Unix/Mac OS), or <a href="https://www.cygwin.com/">Cygwin</a> on windows. See the <a href="{{ url_for("help_item",filename="FAQ")}}">FAQ</a> for details on installing <strong>wget</strong>. </p>
            <ul>
                <li><a href="{{ url_for("download_script", filetype="bam") }}">Download BAMs</a></li>
                <li><a href="{{ url_for("download_script", filetype="cram") }}">Download CRAMs</a></li>
            </ul>
            </p>

        </div>


        <div class="col-md-4">
            <h3>Variant Data</h3>
            <p>We used samtools to identify single-nucleotide variant  (SNV) sites as compared to the N2 reference genome (WS245). Variant data are provided as <abbr data-toggle="tooltip" data-placement="bottom" title="Variant Caller Format">VCF</abbr> or tab-delimited files.</p>

            <p><a href="http://biobits.org/samtools_primer.html#UnderstandingtheVCFFormat" >Learn more about VCF files here</a>.</p>

            <h4>VCF</h4>
            <p>The file below is a single <abbr data-toggle="tooltip" data-placement="bottom" title="Variant Caller Format">VCF</abbr> containing SNVs for all wild isolates.</p>
            <p><a href="https://storage.googleapis.com/andersen_dist/vcf/all/{{ build }}/WI.{{ build }}.snpeff.vcf.gz"><img src="{{ url_for('static',filename = 'img/icons/vcf.png')}}" style="width: 50px; margin-right:20px; margin-bottom:10px;" class="pull-left"></a>
            <strong style="line-height:50px;"><a href="https://storage.googleapis.com/andersen_dist/vcf/all/{{ build }}/WI.{{ build }}.snpeff.vcf.gz">WI.{{ build }}.snpeff.vcf.gz</a></strong></p>

            <div style = "clear:both;"></div>
          
            <p>You can also access specific regions of <abbr data-toggle="tooltip" data-placement="bottom" title="Variant Caller Format">VCF</abbr> files (rather then the entire file) from the command line: <button type="button" class="btn btn-primary btn-xs" data-toggle="modal" data-target="#cli_example">
              See Example
            </button></p>

            <h4>Methods</h4>
            <p>Information regarding alignment, variant calling, and annotation are available <a href="{{ url_for('help_item', filename = "Methods") }}">here</a>.

        </div>
        </br>
        <div class="col-md-4">
                 <div class="panel panel-default">
                        <div class="panel-heading">Strain Data</div>
                        <div class="panel-body">
                            Strain Data including isolation location, isotype information, and more is available for download.<br /><br />
                            <a href="{{ url_for('strain_metadata') }}" type="button" class="btn btn-default btn-block btn-success">Download Strain Data</a>
                        </div>
                    </div>

            <h4>Included Variants</h4>
            <p>Currently, we have performed variant calling across all wild isolates. We are working to add additional variant classes including insertion/deletion, structural, transposon, and additional variant classes.</p>
            <h4>Transposon Data</h4>
            <p>We have recently performed an anaysis characterizing Transposon variation in <em>C. elegans</em>. The dataset will be further integrated with the site resources as time goes on. For now, the raw data are available below.</p>
            <a href="https://storage.googleapis.com/andersenlab.org/publications/2017Laricchia/tes_cender.bed" type="button" class="btn btn-default btn-block btn-success">Download Transposon Data</a>
        </div>
        </div>
        <hr />
        <input id="filter" type="text" class="form-control pull-right" style = "width:200px;" placeholder="Enter Strain Name" action="#">
        <table class="table table-hover table-striped">
            <thead>
                <tr>
                        <th style='width: 20px;'>#</th>
                        <th style="width: 200px;">
                            <span class="tooltip-item" data-toggle="tooltip"  data-placement="bottom" title="Name of strain we distribute as a representative of an isotype.">
                            Reference Strain
                            </span>
                        </th>
                        <th style="width: 200px;">
                            <span class="tooltip-item" data-toggle="tooltip"  data-placement="bottom" title="Name assigned to a group of strains that share the same genome-wide haplotype.">
                            Isotype
                            </span>
                        </th>
                        <th style="width: 200px;">
                        <span class="tooltip-item" data-toggle="tooltip"  data-placement="bottom" title="Individually isolated strains; If strains are assigned to the same isotype they are > 99.93% genetically identical">
                        Strains
                        </span></th>
                    </th>
                    <th style="width: 200px;">BAM</th>
                    <th style="width: 200px;">CRAM</th>
                    <th>Tab-delimited variants</th>
                </tr>
            </thead>
            <div style="height: 30px;" ></div>
            <tbody class="searchable">
                {% for isotype, strains in strain_listing|groupby('isotype') %}
                <tr>
                        <td>{{ loop.index }}</td>
                        <td>
                            {% for s in strains %}
                                {% if s.reference_strain %}
                                    <strong>
                                    {{ s }}
                                    </strong>
                                {% endif %}
                            {% endfor %}
                        </td>

                    <td><a href="{{ url_for('isotype_page', isotype_name=isotype) }}">{{ isotype }}</a></td>
                    <td>{% for s in strains %}
                                {{ s }}
                        {% endfor %}
                    </td>
                    <td>
                        {% if strains[0].bam_file %}
                            <a href="{{ strains[0].bam_file }}">{{ isotype }}.bam</a>
                            <strong>/</strong> <a href="{{ strains[0].bam_index }}">.bai</a> 
                        {% endif %}
                    </td>
                    <td>
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