docs/docs/assays.microbiome.html
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<p>
<a href="index.html">CIDC Documentation</a>
</p>
<h1>
Microbiome Assay
</h1>
<p>
<b>Description:</b> Microbiome Assay.
</p>
</div>
<div class="container">
<div class="accordion" id="assay_accordion">
<div class="card">
<div class="card-header" id="assay_metadata">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#assay_metadata_card" aria-expanded="false" aria-controls="assay_metadata_card">
Assay Metadata
</button>
</h2>
</div>
<div id="assay_metadata_card" class="collapse" aria-labelledby="assay_metadata" data-parent="#assay_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="batch_id">
batch_id
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Microbiome batch identification number.
</td>
<td>
<
string
>
</td>
</tr>
<tr>
<td>
<span id="forward_fastq">
forward_fastq
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Information about a Gzipped FASTQ file.
</td>
<td>
<a href="files.fastq_gz.html">
fastq gz
</a>
</td>
</tr>
<tr>
<td>
<span id="forward_index">
forward_index
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Information about a Gzipped FASTQ file.
</td>
<td>
<a href="files.fastq_gz.html">
fastq gz
</a>
</td>
</tr>
<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="reverse_fastq">
reverse_fastq
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Information about a Gzipped FASTQ file.
</td>
<td>
<a href="files.fastq_gz.html">
fastq gz
</a>
</td>
</tr>
<tr>
<td>
<span id="reverse_index">
reverse_index
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Information about a Gzipped FASTQ file.
</td>
<td>
<a href="files.fastq_gz.html">
fastq gz
</a>
</td>
</tr>
<tr>
<td>
<span id="assay_creator">
assay_creator
</span>
</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="otu_table">
otu_table
</span>
</td>
<td width=55%>
Information about a tab Separated file.
</td>
<td>
<a href="files.tsv.html">
tsv
</a>
</td>
</tr>
<tr>
<td>
<span id="sequencer_platform">
sequencer_platform
</span>
</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="summary_file">
summary_file
</span>
</td>
<td width=55%>
Information about a Portable Document Format file.
</td>
<td>
<a href="files.pdf.html">
pdf
</a>
</td>
</tr>
</table>
</div>
</div>
</div>
<div class="card">
<div class="card-header" id="assay_data">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#assay_data_card" aria-expanded="false" aria-controls="assay_data_card">
Assay Data
</button>
</h2>
</div>
<div id="assay_data_card" class="collapse" aria-labelledby="assay_data" data-parent="#assay_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 colspan=3 class="container">
<div class="accordion" id="records_accordion">
<div class="card">
<div class="card-header" id="records">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#records_card" aria-expanded="false" aria-controls="records_card">
records
</button>
<sup><mark>required</mark></sup>
<div style="float: right;">
<
array
>
</div>
</div>
<div id="records_card" class="collapse" aria-labelledby="records">
<div class="card-body">
A single data record from microbiome assay.
<br>
<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="library_yield_ng">
library_yield_ng
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Resulting yield (in ng) from library construction.
</td>
<td>
<
number
,
string
>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
</td>
</tr>
</table>
</div>
</div>
</div>
<div class="card">
<div class="card-header" id="assay_uploads">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#assay_uploads_card" aria-expanded="false" aria-controls="assay_uploads_card">
Assay Uploads
</button>
</h2>
</div>
<div id="assay_uploads_card" class="collapse" aria-labelledby="assay_uploads" data-parent="#assay_accordion">
<div class="card-body">
<table class="table table-striped">
<thead>
<tr>
<th>Entity</th>
<th>Description</th>
</tr>
</thead>
<tr>
<td width=25%>
<a href='assays.microbiome.microbiome_template.html'>
Metadata file for microbiome.
</a>
</td>
<td>
Metadata information for Microbiome data submission.
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
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