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activities-pas.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 black; 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 #33a02c; background-color: #ffffff">PAS Activities & Counts</button>
</a>
</center>
<br>
<br>
<center>
<div style="width: 60%; text-align: left; border: 2px solid black; background-color: #ffffff; padding: 20px; line-height: 1.5;">
Fitted motif activities as well as calculated activity z-scores and their statistical significance
are stored in a tab-separated formatted (TSV) table.
<br>
Rows of this table denote various sequence motifs in specific sliding windows whereas subsequent columns follow the
structure below:
<br>
<br>
<b>ID</b> : unique ID of a sequence motif in a specific analysis window
<br>
<b>activities_{sampleID}</b> : motif activity in the sampleID sample
<br>
<b>deltas_{sampleID}</b> : delta of motif activity in the sampleID sample
<br>
<b>zscores_{sampleID}</b> : z-score of motif activity in the sampleID sample
<br>
<b>combined.Zscore</b> : overall z-score for a given motif, combined over all samples
<br>
<b>regions_present_fraction</b> : fraction of sites for which the motif was present in a specific analysis window
<br>
<b>region</b> : analysis window ID
<br>
<b>motif</b> : motif name
<br>
<b>standard_zscores_{sampleID}</b> : standardised z-score of motif activity in the sampleID sample
<br>
<b>pval_{sampleID}</b> : standardised p-value of motif activity in the sampleID sample
<br>
<b>corr_pval_{sampleID}</b> : p-values corrected for multiple hypothesis testing
<br>
<b>combined.standard.Zscore</b> : combined standardised z-scores
<br>
<b>max.abs.standard.Zscore</b> : maximum absolute standardised z-score across all samples
<br>
<b>significance-marker</b> : statistical significance marker for this motif in this analysis window
<br>
<br>
Motif count matrices are too storage intensive to provide them as a part of a downloadable MAPP report.
However, you can find them in the following location of your MAPP run: <code>../modules/KAPAC/output</code>,
unless external pre-computed resources were specified for this specific workflow execution.
In such case, please refer to the pipeline's configuration file and inspect the paths you have provided
under the field: <code>KPC_sitecount_matrices</code>.
<br>
<br>
</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/results-pas.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>