docs/docs/assays.atacseq.html
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<p>
<a href="index.html">CIDC Documentation</a>
</p>
<h1>
ATACseq Assay
</h1>
<p>
<b>Description:</b> Assay for Transposase-Accessible Chromatin by Sequencing
</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="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="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="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="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="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="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="bait_set">
bait_set
</span>
</td>
<td width=55%>
Bait set ID.
</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="sequencing_protocol">
sequencing_protocol
</span>
</td>
<td width=55%>
Protocol and version used for the sequencing.
</td>
<td>
<
string
>
</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 ATACseq 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="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="percent_q30">
percent_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>
<tr>
<td>
<span id="sequencing_date">
sequencing_date
</span>
</td>
<td width=55%>
Date of sequencing.
</td>
<td>
<
string
: date
>
</td>
</tr>
<tr>
<td colspan=3 class="container">
<div class="accordion" id="files_accordion">
<div class="card">
<div class="card-header" id="files">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#files_card" aria-expanded="false" aria-controls="files_card">
files
</button>
<sup><mark>required</mark></sup>
<div style="float: right;">
<
object
>
</div>
</div>
<div id="files_card" class="collapse" aria-labelledby="files">
<div class="card-body">
Paired end sequencing in a .fastq file pair or in a .bam
<br>
<table class="table table-striped">
<thead>
<tr>
<th>Property</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<tr>
<td>
<span id="r2">
r2
</span>
</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="r1">
r1
</span>
</td>
<td width=55%>
Fastq file for the first fragment.
</td>
<td>
<a href="files.fastq_gz.html">
fastq gz
</a>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
</td>
</tr>
</table>
</div>
</div>
</div>
<div class="card">
<div class="card-header" id="analysis_metadata">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#analysis_metadata_card" aria-expanded="false" aria-controls="analysis_metadata_card">
Analysis Metadata
</button>
</h2>
</div>
<div id="analysis_metadata_card" class="collapse" aria-labelledby="analysis_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%>
ATACseq batch identification number. Unique to every batch.
</td>
<td>
<
string
>
</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>
</table>
</div>
</div>
</div>
<div class="card">
<div class="card-header" id="analysis_data">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#analysis_data_card" aria-expanded="false" aria-controls="analysis_data_card">
Analysis Data
</button>
</h2>
</div>
<div id="analysis_data_card" class="collapse" aria-labelledby="analysis_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 analysis record from ATACseq analysis.
<br>
<table class="table table-striped">
<thead>
<tr>
<th>Property</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<tr>
<td>
<span id="aligned_sorted_bam">
aligned_sorted_bam
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Information about a BAM file.
</td>
<td>
<a href="files.bam.html">
bam
</a>
</td>
</tr>
<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="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="peaks_accordion">
<div class="card">
<div class="card-header" id="peaks">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#peaks_card" aria-expanded="false" aria-controls="peaks_card">
peaks
</button>
<sup><mark>required</mark></sup>
<div style="float: right;">
<
object
>
</div>
</div>
<div id="peaks_card" class="collapse" aria-labelledby="peaks">
<div class="card-body">
<br>
<table class="table table-striped">
<thead>
<tr>
<th>Property</th>
<th>Description</th>
<th>Data Type</th>
</tr>
</thead>
<tr>
<td>
<span id="sorted_peaks_bed">
sorted_peaks_bed
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Information about a BED file.
</td>
<td>
<a href="files.bed.html">
bed
</a>
</td>
</tr>
<tr>
<td>
<span id="sorted_peaks_narrowpeak">
sorted_peaks_narrowpeak
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Information about a narrowPeak file.
</td>
<td>
<a href="files.narrowPeak.html">
narrowPeak
</a>
</td>
</tr>
<tr>
<td>
<span id="sorted_summits">
sorted_summits
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Information about a BED file.
</td>
<td>
<a href="files.bed.html">
bed
</a>
</td>
</tr>
<tr>
<td>
<span id="treat_pileup">
treat_pileup
</span>
<br><sup><mark>required</mark></sup>
</td>
<td width=55%>
Information about a BIGWIG file.
</td>
<td>
<a href="files.bigwig.html">
bigwig
</a>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
</td>
</tr>
<tr>
<td colspan=3 class="container">
<div class="accordion" id="excluded_samples_accordion">
<div class="card">
<div class="card-header" id="excluded_samples">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#excluded_samples_card" aria-expanded="false" aria-controls="excluded_samples_card">
excluded_samples
</button>
<div style="float: right;">
<
array
>
</div>
</div>
<div id="excluded_samples_card" class="collapse" aria-labelledby="excluded_samples">
<div class="card-body">
A list of samples excluded from analysis, along with the reasons why.
<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="reason_excluded">
reason_excluded
</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>
</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.atacseq.atacseq_fastq_template.html'>
ATACseq [FASTQ] assay template
</a>
</td>
<td>
Assay for Transposase-Accessible Chromatin by Sequencing (ATACseq) data submission via FASTQ files.
</td>
</tr>
</table>
</div>
</div>
</div>
<div class="card">
<div class="card-header" id="analaysis_uploads">
<h2 class="mb-0">
<button class="btn btn-link" type="button" data-toggle="collapse" data-target="#analaysis_uploads_card" aria-expanded="false" aria-controls="analaysis_uploads_card">
Analysis Uploads
</button>
</h2>
</div>
<div id="analaysis_uploads_card" class="collapse" aria-labelledby="analaysis_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.atacseq.atacseq_analysis_template.html'>
ATACseq analysis template
</a>
</td>
<td>
Assay by Transposase-Accessible Chromatin by Sequencing (ATACseq) analysis submission.
</td>
</tr>
</table>
</div>
</div>
</div>
</div>
</div>
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