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exon-inclusion.html
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<!DOCTYPE html>
<html>
<head>
<title>MAPP reports</title>
</head>
<body style="background-color: rgb(219, 219, 219)">
<br>
<center>
<img src=mapp_logo.png width="4%">
<h1>MAPP Report</h1>
<h3>Test run with reduced parameters on a sampled dataset</h3>
<br>
<a href="gene-expression.html" style="text-decoration: none;">
<button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">Gene Expression</button>
</a>
<a href="transcript-expression.html" style="text-decoration: none;">
<button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">Transcript Expression</button>
</a>
<a href="exon-inclusion.html" style="text-decoration: none;">
<button style="width: 180px; height: 40px; border: 2px solid #33a02c; background-color: #ffffff">Exon Inclusion Fractions</button>
</a>
<a href="pas-expression.html" style="text-decoration: none;">
<button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">Poly(A) Site Expressions</button>
</a>
<br>
<br>
<a href="activities-3ss.html" style="text-decoration: none;">
<button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">3'SS Activities & Counts</button>
</a>
<a href="activities-5ss.html" style="text-decoration: none;">
<button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">5'SS Activities & Counts</button>
</a>
<a href="activities-pas.html" style="text-decoration: none;">
<button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">PAS Activities & Counts</button>
</a>
</center>
<br>
<br>
<center>
<div style="width: 50%; text-align: left; border: 2px solid black; background-color: #ffffff; padding: 20px; line-height: 1.5;">
Cassette exon inclusion is represented as a ratio of expression
for transcripts which include a specific exon
to all those transcripts which could have possibly included it.
Numerators and denominators of these ratios are stored in a tab-separated format (TSV) table
in order to still enable TPM-based filtering
Each row in the expression table represents a single cassette exon. The first column
specifies exon coordinates in a BED format.
Each of the next columns stores TPM values for
specific RNA-Seq samples. Columns with numerators of the inclusion fraction ratios are
denoted with an "_included" suffix whereas denominators are marked with "_total".
Please see the scheme below:
<br>
<br>
<center>
<table border="2" style="border-collapse: collapse;">
<tr>
<th style="text-align: center; padding: 5px;"><b></b></th>
<th style="text-align: center; padding: 5px;"><b>Sample1_included</b></th>
<th style="text-align: center; padding: 5px;"><b>Sample2_included</b></th>
<th style="text-align: center; padding: 5px;"><b>...</b></th>
<th style="text-align: center; padding: 5px;"><b>Sample1_total</b></th>
<th style="text-align: center; padding: 5px;"><b>Sample2_total</b></th>
<th style="text-align: center; padding: 5px;"><b>...</b></th>
</tr>
<tr>
<td style="text-align: center; padding: 5px;"><b>Exon1</b></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
</tr>
<tr>
<td style="text-align: center; padding: 5px;"><b>Exon2</b></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
</tr>
<tr>
<td style="text-align: center; padding: 5px;"><b>Exon3</b></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
</tr>
<tr>
<td style="text-align: center; padding: 5px;"><b>...</b></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
</tr>
</table>
</center>
</div>
<br>
<a href="report.html" style="text-decoration: none;">
<button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">Main Menu</button>
</a>
<a href="results/exon-inclusion-table.tsv" style="text-decoration: none;">
<button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">Download Table</button>
</a>
</center>
</body>
</html>