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<p>You can also consult with us for sequencing strategies to determine sequencing depth, read length and pairing mode that will vary greatly depending on the protein of interest and the biological question.</p>
<div class="extra-spaced">
<h2>What do we provide with the analysis?</h2>
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<h3 class="diacol" style="font-weight: 100;">Standard Analysis</h3>
<ul class="square">
<li>Summary statistics (total sequenced reads, total mapping reads, uniquely aligned reads, PCR duplicates, number of peaks, average peak width, reads in peaks, frequency of reads in peaks, etc.)</li>
<li>Trimmed and filtered reads in fastQ files after sequencing QC</li>
<li>BAM sorted files from alignment to reference genome (indexed bam files and bigwig files included)</li>
<li>BED files from peak calling (peak location, peak calling score, peak density)</li>
<li>Annotation files with location of the peaks within genes</li>
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<h3 class="diacol" style="font-weight: 100;">Advanced Analysis</h3>
<ul class="square">
<li>Comparative analysis (also called differential analysis) aimed at finding differentially bound sites or uniquely bound sites between two groups of samples</li>
<li>Annotation of differentially/uniquely bound sites</li>
<li>Determination of specific binding motifs within peaks</li>
<li>Gene ontology enrichment analysis on differentially binding/unique sites</li>
<li>Pathway enrichment analysis (KEGG or DOSE for human samples)</li>
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<p class="text-left">If you require a type of analysis that is not in the previous list, <a href="#" data-reveal-id="quoteModal-3060">please consult with our expert bioinformatics team</a>.</p>
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<h4>ChIP-seq</h4>
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<li>Trimmed and filtered reads in fastQ files after sequencing QC</li>
<li>BAM sorted files from alignment to reference genome (indexed bam files and bigwig files included)</li>
<li>BED files from peak calling (peak location, peak calling score, peak density)</li>
<li>Annotation files with location of the peaks within genes</li>
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<li>Determination of specific binding motifs within peaks</li>
<li>Gene ontology enrichment analysis on differentially binding/unique sites</li>
<li>Pathway enrichment analysis (KEGG or DOSE for human samples)</li>
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<p class="text-left">If you require a type of analysis that is not in the previous list, <a href="#" data-reveal-id="quoteModal-3060">please consult with our expert bioinformatics team</a>.</p>
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Notice (8): Undefined variable: header [APP/View/Products/view.ctp, line 755]Code Context<!-- BEGIN: REQUEST_FORM MODAL -->
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<p>You can also consult with us for sequencing strategies to determine sequencing depth, read length and pairing mode that will vary greatly depending on the protein of interest and the biological question.</p>
<div class="extra-spaced">
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<ul class="square">
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<li>Trimmed and filtered reads in fastQ files after sequencing QC</li>
<li>BAM sorted files from alignment to reference genome (indexed bam files and bigwig files included)</li>
<li>BED files from peak calling (peak location, peak calling score, peak density)</li>
<li>Annotation files with location of the peaks within genes</li>
</ul>
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<ul class="square">
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<li>Annotation of differentially/uniquely bound sites</li>
<li>Determination of specific binding motifs within peaks</li>
<li>Gene ontology enrichment analysis on differentially binding/unique sites</li>
<li>Pathway enrichment analysis (KEGG or DOSE for human samples)</li>
<ul style="list-style-type: circle;"></ul>
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<p class="text-left">If you require a type of analysis that is not in the previous list, <a href="#" data-reveal-id="quoteModal-3060">please consult with our expert bioinformatics team</a>.</p>
</div>
<div class="extra-spaced">
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<center><img src="https://www.diagenode.com/img/product/services/chipseq-schema.png" width="600" height="757" /></center></div>
<div class="extra-spaced">
<h4>ATAC-Seq</h4>
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<p>You can also consult with us for sequencing strategies to determine sequencing depth, read length and pairing mode that will vary greatly depending on the protein of interest and the biological question.</p>
<div class="extra-spaced">
<h2>What do we provide with the analysis?</h2>
<p>This analysis provides information on each region specifically bound by the targeted protein (peak) as well as its level of enrichment (ChIP-seq) or openness (ATAC-seq).</p>
<h3 class="diacol" style="font-weight: 100;">Standard Analysis</h3>
<ul class="square">
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<li>Trimmed and filtered reads in fastQ files after sequencing QC</li>
<li>BAM sorted files from alignment to reference genome (indexed bam files and bigwig files included)</li>
<li>BED files from peak calling (peak location, peak calling score, peak density)</li>
<li>Annotation files with location of the peaks within genes</li>
</ul>
<h3 class="diacol" style="font-weight: 100;">Advanced Analysis</h3>
<ul class="square">
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<li>Annotation of differentially/uniquely bound sites</li>
<li>Determination of specific binding motifs within peaks</li>
<li>Gene ontology enrichment analysis on differentially binding/unique sites</li>
<li>Pathway enrichment analysis (KEGG or DOSE for human samples)</li>
<ul style="list-style-type: circle;"></ul>
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<p class="text-left">If you require a type of analysis that is not in the previous list, <a href="#" data-reveal-id="quoteModal-3060">please consult with our expert bioinformatics team</a>.</p>
</div>
<div class="extra-spaced">
<h4>ChIP-seq</h4>
<center><img src="https://www.diagenode.com/img/product/services/chipseq-schema.png" width="600" height="757" /></center></div>
<div class="extra-spaced">
<h4>ATAC-Seq</h4>
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<h3 class="diacol" style="font-weight: 100;">Standard Analysis</h3>
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<li>Trimmed and filtered reads in fastQ files after sequencing QC</li>
<li>BAM sorted files from alignment to reference genome (indexed bam files and bigwig files included)</li>
<li>BED files from peak calling (peak location, peak calling score, peak density)</li>
<li>Annotation files with location of the peaks within genes</li>
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<li>Comparative analysis (also called differential analysis) aimed at finding differentially bound sites or uniquely bound sites between two groups of samples</li>
<li>Annotation of differentially/uniquely bound sites</li>
<li>Determination of specific binding motifs within peaks</li>
<li>Gene ontology enrichment analysis on differentially binding/unique sites</li>
<li>Pathway enrichment analysis (KEGG or DOSE for human samples)</li>
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<li>Trimmed and filtered reads in fastQ files after sequencing QC</li>
<li>BAM sorted files from alignment to reference genome (indexed bam files and bigwig files included)</li>
<li>BED files from peak calling (peak location, peak calling score, peak density)</li>
<li>Annotation files with location of the peaks within genes</li>
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<li>Determination of specific binding motifs within peaks</li>
<li>Gene ontology enrichment analysis on differentially binding/unique sites</li>
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Notice (8): Undefined variable: campaign_id [APP/View/Products/view.ctp, line 755]Code Context<!-- BEGIN: REQUEST_FORM MODAL -->
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<p>You can also consult with us for sequencing strategies to determine sequencing depth, read length and pairing mode that will vary greatly depending on the protein of interest and the biological question.</p>
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<li>Trimmed and filtered reads in fastQ files after sequencing QC</li>
<li>BAM sorted files from alignment to reference genome (indexed bam files and bigwig files included)</li>
<li>BED files from peak calling (peak location, peak calling score, peak density)</li>
<li>Annotation files with location of the peaks within genes</li>
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<h3 class="diacol" style="font-weight: 100;">Advanced Analysis</h3>
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<li>Annotation of differentially/uniquely bound sites</li>
<li>Determination of specific binding motifs within peaks</li>
<li>Gene ontology enrichment analysis on differentially binding/unique sites</li>
<li>Pathway enrichment analysis (KEGG or DOSE for human samples)</li>
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<p class="text-left">If you require a type of analysis that is not in the previous list, <a href="#" data-reveal-id="quoteModal-3060">please consult with our expert bioinformatics team</a>.</p>
</div>
<div class="extra-spaced">
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<center><img src="https://www.diagenode.com/img/product/services/chipseq-schema.png" width="600" height="757" /></center></div>
<div class="extra-spaced">
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<p>You can also consult with us for sequencing strategies to determine sequencing depth, read length and pairing mode that will vary greatly depending on the protein of interest and the biological question.</p>
<div class="extra-spaced">
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<li>Trimmed and filtered reads in fastQ files after sequencing QC</li>
<li>BAM sorted files from alignment to reference genome (indexed bam files and bigwig files included)</li>
<li>BED files from peak calling (peak location, peak calling score, peak density)</li>
<li>Annotation files with location of the peaks within genes</li>
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<li>Determination of specific binding motifs within peaks</li>
<li>Gene ontology enrichment analysis on differentially binding/unique sites</li>
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<p class="text-left">If you require a type of analysis that is not in the previous list, <a href="#" data-reveal-id="quoteModal-3060">please consult with our expert bioinformatics team</a>.</p>
</div>
<div class="extra-spaced">
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<center><img src="https://www.diagenode.com/img/product/services/chipseq-schema.png" width="600" height="757" /></center></div>
<div class="extra-spaced">
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Controller::invokeAction() - CORE/Cake/Controller/Controller.php, line 491
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 193
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 167
[main] - APP/webroot/index.php, line 118
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