docs/docs/assays.atacseq.atacseq_analysis_template.html
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<p>
<a href="index.html">CIDC Documentation</a>
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<h1>
ATACseq analysis template
</h1>
<p>
<b>Description:</b> Assay by Transposase-Accessible Chromatin by Sequencing (ATACseq) analysis submission.
</p>
</div>
<div class="container">
<div class="accordion" id="ATACseq_Analysis_accordion">
<div class="card">
<div class="card-header" id="ATACseq_Analysis">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#ATACseq_Analysis_card" aria-expanded="false" aria-controls="ATACseq_Analysis_card">
Worksheet - ATACseq Analysis
</button>
</h2>
</div>
<div id="ATACseq_Analysis_card" class="collapse" aria-labelledby="ATACseq_Analysis" data-parent="#ATACseq_Analysis_accordion">
<div class="card-body">
<div class="accordion" id="ATACseq_Analysis_preamble_accordion">
<div class="card">
<div class="card-header" id="ATACseq_Analysis_preamble">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#ATACseq_Analysis_preamble_card" aria-expanded="false" aria-controls="ATACseq_Analysis_preamble_card">
Preamble Rows
</button>
</h2>
</div>
<div id="ATACseq_Analysis_preamble_card" class="collapse" aria-labelledby="ATACseq_Analysis_preamble" data-parent="#ATACseq_Analysis_preamble_accordion">
<div class="card-body">
<table class="table table-striped">
<thead>
<tr>
<th>Property</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<tr>
<td>
<span id="protocol identifier">
protocol identifier
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Trial identifier used by lead organization, ie. Center for Experimental Therapeutics Program (CTEP) ID or Industry Sponsored ID. This is usually a short identifier. Example: E4412.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="batch id">
batch id
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
ATACseq batch identification number. Unique to every batch.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="folder">
folder
</span>
</td>
<td width=55%>
</td>
<td>
<
string
>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
<div class="accordion" id="ATACseq_Analysis_body_accordion">
<div class="card">
<div class="card-header" id="ATACseq_Analysis_body">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#ATACseq_Analysis_body_card" aria-expanded="false" aria-controls="ATACseq_Analysis_body_card">
Data Columns
</button>
</h2>
</div>
<div id="ATACseq_Analysis_body_card" class="collapse" aria-labelledby="ATACseq_Analysis_body" data-parent="#ATACseq_Analysis_body_accordion">
<div class="card-body">
<h5 class="text-muted">ATACseq Runs</h4>
<table class="table table-striped">
<thead>
<tr>
<th>Property</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<tr>
<td>
<span id="comments">
comments
</span>
</td>
<td width=55%>
Comments on the ATACseq analysis run.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td colspan=3 class="container">
<div class="accordion" id="cimac_id_accordion">
<div class="card">
<div class="card-header" id="cimac_id">
<div class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#cimac_id_card" aria-expanded="false" aria-controls="cimac_id_card">
cimac id
</button>
<sup><mark>required</mark></sup>
<div style="float: right;">
<
string
>
</div>
</div>
</div>
<div id="cimac_id_card" class="collapse" aria-labelledby="cimac_id">
<div class="card-body">
Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as CTTTPPPSS.AA for trial code TTT, participant PPP, sample SS, and aliquot AA.
<br>
All files are
<sup><mark>required</mark></sup>
<br>
<table class="table table-striped">
<thead>
<tr>
<th>File name</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<tr>
<td>
{folder or ""}analysis/peaks/{id}.rep1/{id}.rep1_sorted_peaks.bed
</td>
<td width=55%>
Information about a BED file.
</td>
<td>
<a href="files.bed.html">
bed
</a>
</td>
</tr>
<tr>
<td>
{folder or ""}analysis/peaks/{id}.rep1/{id}.rep1_sorted_summits.bed
</td>
<td width=55%>
Information about a BED file.
</td>
<td>
<a href="files.bed.html">
bed
</a>
</td>
</tr>
<tr>
<td>
{folder or ""}analysis/peaks/{id}.rep1/{id}.rep1_sorted_peaks.narrowPeak
</td>
<td width=55%>
Information about a narrowPeak file.
</td>
<td>
<a href="files.narrowPeak.html">
narrowPeak
</a>
</td>
</tr>
<tr>
<td>
{folder or ""}analysis/peaks/{id}.rep1/{id}.rep1_treat_pileup.bw
</td>
<td width=55%>
Information about a BIGWIG file.
</td>
<td>
<a href="files.bigwig.html">
bigwig
</a>
</td>
</tr>
<tr>
<td>
{folder or ""}analysis/align/{id}/{id}.sorted.bam
</td>
<td width=55%>
Information about a BAM file.
</td>
<td>
<a href="files.bam.html">
bam
</a>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<div class="accordion" id="Excluded_Samples_accordion">
<div class="card">
<div class="card-header" id="Excluded_Samples">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#Excluded_Samples_card" aria-expanded="false" aria-controls="Excluded_Samples_card">
Worksheet - Excluded Samples
</button>
</h2>
</div>
<div id="Excluded_Samples_card" class="collapse" aria-labelledby="Excluded_Samples" data-parent="#Excluded_Samples_accordion">
<div class="card-body">
<div class="accordion" id="Excluded_Samples_body_accordion">
<div class="card">
<div class="card-header" id="Excluded_Samples_body">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#Excluded_Samples_body_card" aria-expanded="false" aria-controls="Excluded_Samples_body_card">
Data Columns
</button>
</h2>
</div>
<div id="Excluded_Samples_body_card" class="collapse" aria-labelledby="Excluded_Samples_body" data-parent="#Excluded_Samples_body_accordion">
<div class="card-body">
<h5 class="text-muted">Samples Excluded From Analysis</h4>
<table class="table table-striped">
<thead>
<tr>
<th>Property</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<tr>
<td>
<span id="cimac id">
cimac id
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Specimen identifier assigned by the CIMAC-CIDC Network. Formatted as CTTTPPPSS.AA for trial code TTT, participant PPP, sample SS, and aliquot AA.
</td>
<td>
<
string
>
as regex <br> <code>^C[A-Z0-9]{3}[A-Z0-9]{3}[A-Z0-9]{2}.[0-9]{2}$</code>
</td>
</tr>
<tr>
<td>
<span id="reason">
reason
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
A comment describing why this sample is missing from the pipeline output.
</td>
<td>
<
string
>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
</div>
</div>
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