docs/docs/assays.atacseq.atacseq_fastq_template.html
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<a href="index.html">CIDC Documentation</a>
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<h1>
ATACseq [FASTQ] assay template
</h1>
<p>
<b>Description:</b> Assay for Transposase-Accessible Chromatin by Sequencing (ATACseq) data submission via FASTQ files.
</p>
</div>
<div class="container">
<div class="accordion" id="ATACseq_accordion">
<div class="card">
<div class="card-header" id="ATACseq">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#ATACseq_card" aria-expanded="false" aria-controls="ATACseq_card">
Worksheet - ATACseq
</button>
</h2>
</div>
<div id="ATACseq_card" class="collapse" aria-labelledby="ATACseq" data-parent="#ATACseq_accordion">
<div class="card-body">
<div class="accordion" id="ATACseq_preamble_accordion">
<div class="card">
<div class="card-header" id="ATACseq_preamble">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#ATACseq_preamble_card" aria-expanded="false" aria-controls="ATACseq_preamble_card">
Preamble Rows
</button>
</h2>
</div>
<div id="ATACseq_preamble_card" class="collapse" aria-labelledby="ATACseq_preamble" data-parent="#ATACseq_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="assay creator">
assay creator
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Indicates what site is filling out the assay.
</td>
<td>
<
string
>
<ul>
<li>"DFCI"</li>
<li>"Mount Sinai"</li>
<li>"Stanford"</li>
<li>"MD Anderson"</li>
<li>"Adaptive"</li>
<li>"Broad"</li>
</ul>
</td>
</tr>
<tr>
<td>
<span id="sequencer platform">
sequencer platform
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Sequencer Model, e.g. HiSeq 2500, NextSeq, NovaSeq.
</td>
<td>
<
string
>
<ul>
<li>"Adaptive"</li>
<li>"Illumina - HiSeq 2500"</li>
<li>"Illumina - HiSeq 3000"</li>
<li>"Illumina - NextSeq 550"</li>
<li>"Illumina - HiSeq 4000"</li>
<li>"Illumina - NovaSeq 6000"</li>
<li>"MiSeq"</li>
</ul>
</td>
</tr>
<tr>
<td>
<span id="paired end reads">
paired end reads
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Indicates if the sequencing was performed paired or single ended.
</td>
<td>
<
string
>
<ul>
<li>"Paired"</li>
<li>"Single"</li>
</ul>
</td>
</tr>
<tr>
<td>
<span id="read length">
read length
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Number of cycles for each sequencing read.
</td>
<td>
<
integer
>
</td>
</tr>
<tr>
<td>
<span id="sequencing protocol">
sequencing protocol
</span>
</td>
<td width=55%>
Protocol and version used for the sequencing.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="library kit">
library kit
</span>
</td>
<td width=55%>
The library construction kit.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="bait set">
bait set
</span>
</td>
<td width=55%>
Bait set ID.
</td>
<td>
<
string
>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
<div class="accordion" id="ATACseq_body_accordion">
<div class="card">
<div class="card-header" id="ATACseq_body">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#ATACseq_body_card" aria-expanded="false" aria-controls="ATACseq_body_card">
Data Columns
</button>
</h2>
</div>
<div id="ATACseq_body_card" class="collapse" aria-labelledby="ATACseq_body" data-parent="#ATACseq_body_accordion">
<div class="card-body">
<h5 class="text-muted">Samples</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="lane">
lane
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="replicate number">
replicate number
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
A unique number specifying the replicate.
</td>
<td>
<
integer
>
</td>
</tr>
<tr>
<td>
<span id="forward fastq">
forward fastq
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Fastq file for the first fragment.
</td>
<td>
<a href="files.fastq_gz.html">
fastq gz
</a>
</td>
</tr>
<tr>
<td>
<span id="reverse fastq">
reverse fastq
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Fastq file for the second fragment.
</td>
<td>
<a href="files.fastq_gz.html">
fastq gz
</a>
</td>
</tr>
<tr>
<td>
<span id="sequencing date">
sequencing date
</span>
</td>
<td width=55%>
Date of sequencing.
</td>
<td>
<
string
: date
>
</td>
</tr>
<tr>
<td>
<span id="%Q30">
%Q30
</span>
</td>
<td width=55%>
One quantitative measure of the sequencing accuracy.
</td>
<td>
<
number
>
</td>
</tr>
<tr>
<td>
<span id="quality flag">
quality flag
</span>
</td>
<td width=55%>
Flag used for quality.
</td>
<td>
<
number
>
</td>
</tr>
</table>
</div>
</div>
</div>
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