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Input files
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Contigs
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Nb. of seq. by feature type
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Contigs len. distribution
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Features len. distribution
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Reads
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Intron extraction results
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Split reads
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Detected introns
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Filtered detected introns
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Contigs with too complex introns
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Evaluation of the detected introns (simulation only)
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Glossary
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Produced by IntronSeeker_v1.0<br>
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<h1 class="h4">Input files</h1>
<span class="anchor" id="inputs-parameters"></span>
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<div class="d-flex">
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<h5>Files</h5>
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<li class="list-group-item d-flex justify-content-between align-items-center p-2">Contig FASTA <span class="badge badge-success badge-pill ml-4">Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.dna.toplevel.fa</span></li>
<li class="list-group-item d-flex justify-content-between align-items-center p-2">Contig FASTA with feature(s) <span class="badge badge-success badge-pill ml-4">gbs_Ggal_transcripts-modified.fa</span></li>
<li class="list-group-item d-flex justify-content-between align-items-center p-2">GTF of contig with feature(s) <span class="badge badge-success badge-pill ml-4">gbs_Ggal_transcripts-modified.gtf</span></li>
<li class="list-group-item d-flex justify-content-between align-items-center p-2">Read1 FASTQ <span class="badge badge-success badge-pill ml-4">sr_Ggal_R1.fastq.gz</span></li>
<li class="list-group-item d-flex justify-content-between align-items-center p-2">Read2 FASTQ <span class="badge badge-success badge-pill ml-4">sr_Ggal_R2.fastq.gz</span></li>
<li class="list-group-item d-flex justify-content-between align-items-center p-2">Ranks <span class="badge badge-success badge-pill ml-4">sr_Ggal_ranks.txt</span></li>
<li class="list-group-item d-flex justify-content-between align-items-center p-2">Flagstat <span class="badge badge-success badge-pill ml-4">hisat2_Ggal.sort.flagstat.txt</span></li>
<li class="list-group-item d-flex justify-content-between align-items-center p-2">Split <span class="badge badge-success badge-pill ml-4">srs_Ggal_split_alignments.txt</span></li>
<li class="list-group-item d-flex justify-content-between align-items-center p-2">Candidat <span class="badge badge-success badge-pill ml-4">srs_Ggal_candidates.txt</span></li>
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<div class="d-flex justify-content-between flex-wrap flex-md-nowrap align-items-center mt-5 pb-2 border-bottom">
<h1 class="h4">Contigs</h1>
<span class="anchor" id="ref-descr"></span>
</div>
<div class="d-flex">
<div class="mt-4 mr-0 pl-0 col-md-4">
<div class="d-flex">
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<h5>Contigs statistics</h5>
<span class="anchor" id="ref-descr"></span>
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<div class="ml-2">
<span
class="badge badge-pill badge-dark"
data-toggle="tooltip"
data-placement="top"
data-html="true"
title="<p nowrap><b>Number of features in GTF</b>: total number of features from GTF file</p><p nowrap><b>Number of distinct features in GTF</b>: number of distinct features from all GTF lines</p>">
<span class="oi oi-info" ></span>
</span>
</div>
</div>
<table class="table table-striped table-bordered table-sm mb-0 " style="width:100%">
<tbody>
<tr><td class='valn'>1Contig FASTA - Number of sequences</td><td class='valn text-right'>214</td></tr><tr><td class='valn'>2Contig FASTA - Mean sequence length</td><td class='valn text-right'>4 922 113</td></tr><tr><td class='valn'>3Contig FASTA with feature(s) - Number of sequences</td><td class='valn text-right'>21 590</td></tr><tr><td class='valn'>4Contig FASTA with feature(s) - Mean sequence length</td><td class='valn text-right'>4 164</td></tr><tr><td class='valn'>5Number of modified sequences</td><td class='valn text-right'>8 427</td></tr><tr><td class='valn'>6Number of distinct features in GTF</td><td class='valn text-right'>1</td></tr><tr><td class='valn'>7Number of features in GTF</td><td class='valn text-right'>13 857</td></tr><tr><td class='valn text-right'>retained_intron (s) </td><td class='valn text-right'>13 857</td></tr></tbody></table>
</div>
<div class="mt-4 mr-0 pl-0 col-md-4">
<div class="d-flex">
<div>
<h5>Number of sequences by feature type</h5>
<span class="anchor" id="ref-descr"></span>
</div>
<div class="ml-2">
<span
class="badge badge-pill badge-dark"
data-toggle="tooltip"
data-placement="top"
data-html="true"
title="<p nowrap><b>Number of ctg by feature from all GTF lines </b> (Ex: 'Exon' see in X ctg, 'Intron' see in Y ctg, ...)</p>">
<span class="oi oi-info"></span>
</span>
</div>
</div>
<table class="table table-striped table-bordered table-sm mb-0 " style="width:100%">
<tbody>
<tr><td class='valn'>retained_intron</td><td class='valn text-right'>8 427</td></tr></tbody></table>
</div>
<div class="mt-4 mr-0 pl-0 col-md-4">
<div class="d-flex">
<div>
<h5>Number of sequences with same feature(s)</h5>
<span class="anchor" id="ref-descr"></span>
</div>
<div class="ml-2">
<span
class="badge badge-pill badge-dark"
data-toggle="tooltip"
data-placement="top"
data-html="true"
title="<p nowrap><b>Number of features profiles by ctg </b>(Ex: '1 Exon & 2 Intron' see in X ctg, '3 Introns' see in Y ctg , ...)</p>">
<span class="oi oi-info"></span>
</span>
</div>
</div>
<table class="table table-striped table-bordered table-sm mb-0 " style="width:100%">
<tbody>
<tr><td class='valn'>1 retained_intron</td><td class='valn text-right'>4 642</td></tr><tr><td class='valn'>2 retained_intron</td><td class='valn text-right'>2 140</td></tr><tr><td class='valn'>3 retained_intron</td><td class='valn text-right'>1 645</td></tr></tbody></table>
</div>
</div>
<div class="d-flex">
<div class="mt-4 mr-0 pl-0 col-md-6">
<h5>Assemblathon statistics</h5>
<span class="anchor" id="ref-descr_assemblathon_fasta"></span>
<table class="table table-striped table-bordered table-sm mb-0 " style="width:100%">
<thead>
<tr><td width='33%'></td><td class='valn text-center' width='33%'>Contig FASTA</td><td class='valn text-center' width='33%'>Contig FASTA with feature(s)</td></tr></thead><tbody><tr><td class='valn text-left'>Number of contigs</td><td class='valn text-right'>660</td><td class='valn text-right'>21 596</td></tr><tr><td class='valn text-left'>Mean contigs length</td><td class='valn text-right'>1 590 831</td><td class='valn text-right'>4 163</td></tr><tr><td class='valn text-left'>Total size of contigs</td><td class='valn text-right'>1 049 948 559</td><td class='valn text-right'>89 913 280</td></tr><tr><td class='valn text-left'>Longest contig</td><td class='valn text-right'>65 391 699</td><td class='valn text-right'>106 915</td></tr><tr><td class='valn text-left'>Shortest contig</td><td class='valn text-right'>1 214</td><td class='valn text-right'>78</td></tr><tr><td class='valn text-left'>Number of contigs > 1K nt</td><td class='valn text-right'>660</td><td class='valn text-right'>19 915</td></tr><tr><td class='valn text-left'>N50 contig length</td><td class='valn text-right'>22 526 059</td><td class='valn text-right'>5 157</td></tr><tr><td class='valn text-left'>L50 contig count</td><td class='valn text-right'>17</td><td class='valn text-right'>4 526</td></tr></tbody></table>
</div>
</div>
<div class="mt-4 mr-0 pl-0 col-md-12">
<h5>Contigs length distribution</h5>
<span class="anchor" id="contigs_len_dist"></span>
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</div>
<div class="d-flex">
<div class="mt-4 mr-0 pl-0 col-md-6">
<h5>Features length distribution</h5>
<span class="anchor" id="feat_len_dist"></span>
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<div class="mt-4 mr-0 pl-0 col-md-6">
<h5>Insertion position of introns along contigs</h5>
<span class="anchor" id="feat_dist_intron"></span>
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</div>
</div>
<div class="d-flex justify-content-between flex-wrap flex-md-nowrap align-items-center mt-5 pb-2 border-bottom">
<h1 class="h4">Reads</h1>
<span class="anchor" id="read-descr"></span>
</div>
<div class="d-flex">
<div class="mt-4 mr-4 pl-0 col-md-4">
<h5>Reads statistics</h5>
<span class="anchor" id="readgstat"></span>
<table class="table table-striped table-bordered table-sm mb-0 " style="width:100%">
<tbody>
<tr><td class='valn'>Number of reads</td><td class='valn text-right'>100 000</td></tr><tr><td class='valn'>Mean coverage</td><td class='valn text-right'>0.01</td></tr><tr><td class='valn'>Min reads length</td><td class='valn text-right'>67</td></tr><tr><td class='valn'>Max reads length</td><td class='valn text-right'>136</td></tr><tr><td class='valn'>Mean reads length</td><td class='valn text-right'>99.99</td></tr></tbody></table>
</div>
<div class="mt-4 mr-0 pl-0 col-md-8">
<h5>Reads length distribution</h5>
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</div>
</div>
<div class="d-flex justify-content-between flex-wrap flex-md-nowrap align-items-center mt-5 pb-2 border-bottom">
<h1 class="h4">Mapping (QC-passed reads)</h1>
<span class="anchor" id="flag-descr"></span>
</div>
<div class="d-flex">
<div class="mt-4 mr-0 pl-0 col-md-4">
<table class="table table-striped table-bordered table-sm mb-0 " style="width:100%">
<tbody>
<tr><td class='valn'>Number of reads</td><td class='valn text-right'>100 000</td></tr><tr><td class='valn'>Number of lines in the BAM</td><td class='valn text-right'>103 579</td></tr><tr><td class='valn'>Number of mapped reads</td><td class='valn text-right'>5 461</td></tr><tr><td class='valn'>Percentage of mapped reads</td><td class='valn text-right'>5.46</td></tr><tr><td class='valn'>Number of properly paired reads</td><td class='valn text-right'>3 422</td></tr><tr><td class='valn'>Percentage of properly paired reads</td><td class='valn text-right'>3.42</td></tr><tr><td class='valn'>Secondary alignments</td><td class='valn text-right'>3 579</td></tr><tr><td class='valn'>Singletons alignements</td><td class='valn text-right'>1 613</td></tr></tbody></table>
</div>
</div>
<div class="d-flex justify-content-between flex-wrap flex-md-nowrap align-items-center mt-5 pb-2 border-bottom">
<h1 class="h4">Intron extraction results</h1>
<span class="anchor" id="features-descr"></span>
</div>
<div class="d-flex">
<div class="mt-4 mr-0 pl-0 col-md-4">
<h5>Split reads</h5>
<span class="anchor" id="splitstat"></span>
<table class="table table-striped table-bordered table-sm mb-0 " style="width:100%">
<tbody>
<tr><td class='valn'>Number of reads overlapping introns</td><td class='valn text-right'>6</td></tr><tr><td class='valn'>Mean length of introns</td><td class='valn text-right'>2691.83</td></tr><tr><td class='valn text-right'>Junction GG_GT</td><td class='valn text-right'>1</td></tr><tr><td class='valn text-right'>Other junctions</td><td class='valn text-right'>0</td></tr><tr><td class='valn text-right'>Canonical junction (GT_AG or CT_AC)</td><td class='valn text-right'>5</td></tr></tbody></table>
</div>
</div>
<div class="d-flex">
<div class="mt-4 mr-0 pl-0 col-md-4">
<h5>Detected introns</h5>
<span class="anchor" id="candidatstat"></span>
<table class="table table-striped table-bordered table-sm mb-0 " style="width:100%">
<tbody>
<tr><td class='valn'>Number</td><td class='valn text-right'>6</td></tr><tr><td class='valn'>Min length</td><td class='valn text-right'>20</td></tr><tr><td class='valn'>Max length</td><td class='valn text-right'>6 785</td></tr><tr><td class='valn'>Mean length</td><td class='valn text-right'>2691.83</td></tr><tr><td class='valn'>Min depth</td><td class='valn text-right'>1</td></tr><tr><td class='valn'>Max depth</td><td class='valn text-right'>1</td></tr><tr><td class='valn'>Mean depth</td><td class='valn text-right'>1.0</td></tr></tbody></table>
</div>
<div class="mt-4 mr-0 pl-0 col-md-8">
<h5>Detected introns depth distribution</h5>
<span class="anchor" id="candidatstat"></span>
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introns depth"}},"yaxis":{"title":{"text":"Number of detected introns"}}}, {"responsive": true} ) }; </script> </div>
</div>
</div>
<div class="d-flex">
<div class="mt-4 mr-0 pl-0 col-md-8">
<h5>Filtered detected introns and filtered features (detectable)</h5>
<span class="anchor" id="filtered_detected_introns"></span>
<table class="table table-striped table-bordered table-sm mb-0 " style="width:100%">
<thead>
<tr><td width='33%'></td><td class='valn text-center' width='33%'>Filtered detected introns</td><td class='valn text-center' width='33%'>Filtered features (detectable)</td></tr></thead><tbody><tr><td class='valn text-left'>Number</td><td class='valn text-right'>0</td><td class='valn text-right'>0</td></tr><tr><td class='valn text-left'>Filtered because of depth (<= 1)</td><td class='valn text-right'>6</td><td class='valn text-right'>13 857</td></tr><tr><td class='valn text-left'>Filtered because of length (>= 80%)</td><td class='valn text-right'>0</td><td class='valn text-right'>39</td></tr><tr><td class='valn text-left'>Filtered because of non canonical junction</td><td class='valn text-right'>1</td><td class='valn text-right'>690</td></tr><tr><td class='valn text-left'>Filtered because of overlapping introns</td><td class='valn text-right'>0</td><td class='valn text-right'>-</td></tr><tr><td class='valn text-left'>Min length</td><td class='valn text-right'>99 999 999</td><td class='valn text-right'>99 999 999</td></tr><tr><td class='valn text-left'>Max length</td><td class='valn text-right'>0</td><td class='valn text-right'>0</td></tr><tr><td class='valn text-left'>Mean length</td><td class='valn text-right'>NaN</td><td class='valn text-right'>NaN</td></tr><tr><td class='valn text-left'>Min depth</td><td class='valn text-right'>99 999 999</td><td class='valn text-right'>99 999 999</td></tr><tr><td class='valn text-left'>Max depth</td><td class='valn text-right'>0</td><td class='valn text-right'>0</td></tr><tr><td class='valn text-left'>Mean depth</td><td class='valn text-right'>NaN</td><td class='valn text-right'>NaN</td></tr></tbody></table>
</div>
</div>
<div class="d-flex">
<div class="mt-4 mr-0 pl-0 col-md-4">
<h5>Top 10 of contigs with the highest number of detected introns</h5>
<span class="anchor" id="too_complex_detected"></span>
<table class="table table-striped table-bordered table-sm mb-0 " style="width:100%">
<tbody>
</tbody></table>
</div>
</div>
<div class="d-flex justify-content-between flex-wrap flex-md-nowrap align-items-center mt-5 pb-2 border-bottom">
<h1 class="h4">Evaluation of the detected introns</h1>
<span class="anchor" id="eval"></span>
</div>
<div class="d-flex">
<div class="mt-4 mr-0 pl-0 col-md-8">
<table class="table table-striped table-bordered table-sm mb-0 " style="width:100%">
<thead>
<tr><td width='33%'></td><td class='valn text-center' width='33%'>Raw</td><td class='valn text-center' width='33%'>Filtered</td></tr></thead><tbody><tr><td class='valn text-left'>Number of detected introns</td><td class='valn text-right'>6</td><td class='valn text-right'>0</td></tr><tr><td class='valn text-left'>Number of features</td><td class='valn text-right'>13 857</td><td class='valn text-right'>0</td></tr><tr><td class='valn text-left'>TP = Detected introns ∩ Features</td><td class='valn text-right'>0</td><td class='valn text-right'>0</td></tr><tr><td class='valn text-left'>FP = Detected introns ∉ Features</td><td class='valn text-right'>6</td><td class='valn text-right'>0</td></tr><tr><td class='valn text-left'>FN = Features ∉ Detected introns</td><td class='valn text-right'>13 857</td><td class='valn text-right'>0</td></tr><tr><td class='valn text-left'>Sensibility (Se) = TP / (TP+FN)</td><td class='valn text-right'>0.0</td><td class='valn text-right'>NaN</td></tr><tr><td class='valn text-left'>Specificity (Sp) = TP / (TP+FP)</td><td class='valn text-right'>0.0</td><td class='valn text-right'>NaN</td></tr><tr><td class='valn text-left'>F1 score = (2*Se*Sp) / (Se+Sp)</td><td class='valn text-right'>NaN</td><td class='valn text-right'>NaN</td></tr></tbody></table>
</div>
</div>
<div class="d-flex justify-content-between flex-wrap flex-md-nowrap align-items-center mt-5 pb-2 border-bottom">
<h1 class="h4">Glossary</h1>
<span class="anchor" id="glossary"></span>
</div>
<div class="d-flex">
<div class="mt-4 mr-0 pl-0 col-md-12">
<span class="anchor" id="glossary"></span>
This glossary reflects terms used in this report:<br>
<strong>Candidat</strong> : Detected/predicted introns filtrered by canonical junction, length and depth.</br>
<strong>Canonic junction</strong>: GT_AG or CT_AC for donor and acceptor sites.</br>
<strong>Contig</strong> : A set of overlapping DNA segments that together represent a consensus region of DNA (source :Wikipedia)</br>
<strong>Exon</strong> : Coding part of DNA that is translated into protein.</br>
<strong>Features</strong> : A sequenced chain of nucleic acids which provide protein(s). (source:https://biologydictionary.net/gene/)</br>
<strong>Fragment</strong> : During sequencing, the fragment is a link between fowarded and reverse reads.</br>
<strong>Intron</strong> : Any nucleotide sequence removed by RNA splicing during maturation of RNA. (source : Wikipedia)</br>
<strong>Reads</strong> : An inferred sequence of base pairs corresponding to all or part of a single DNA fragment. (source : Wikipedia)</br>
<strong>Sequence</strong> : Base pair probabilities of a DNA fragment.</br>
<strong>Splice events</strong> : a process where exons may be included within or excluded from the final mRNA.</br>
<strong>Trimmed contig</strong> : Contig without retained intron(s).</br>
<br>
<img src="https://forgemia.inra.fr/emilien.lasguignes/intronSeeker/-/raw/master/doc/IntronSeeker-glossary.png" alt="intronSeeker glossary" style="width:825;height:245;">
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