108 lines
5.8 KiB
HTML
108 lines
5.8 KiB
HTML
<!DOCTYPE html>
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<!-- $Id: BAMDemo.html 47770 2024-07-25 18:40:49Z evgeniev $ -->
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<head >
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<title>NCBI Sequence Viewer 3.50.0 Remote (HTTP-hosted) BAM files Demo</title>
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h2 {
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<body >
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<div id="header"></div>
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<nav class="ncbi-topnav">
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<ul class="ncbi-topnav-list">
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<li><a href="." target="_self">NCBI Sequence Viewer Home</a></li>
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<li><a href="/tools/sviewer" target="_blank">Help</a></li>
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<li><a href="/tools/sviewer/release-notes" target="_blank">Release Notes</a></li>
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<main id="main_content" accesskey="3">
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<div class="content">
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<h1>Remote BAM files Demo</h1>
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<h2>Introduction</h2>
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<p/>
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These examples demonstrate visualization of BAM alignments in the NCBI Sequence Viewer.<br>
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Sequence Viewer supports three levels of zoom detail: coverage graph, match-mismatch pileup and display of BAM reads.<br>
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Sequence Viewer also supports grouping of reads by strand and <a href="BAMhaplotypeDemo.html">haplotype</a>.
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<p/>
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<p/>
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<h3>Example 1</h3>
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<p/>
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Homo sapiens: chromosome 19, assembly GRCh38.p14 (<a href="https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.40">https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.40</a>)<br>
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BAM file is hosted at http://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh38/rnaseq/GRCh38.illumina.brain.1.bam
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<div id="SViewer0" class="SeqViewerApp" data-autoload><a href="?embedded=full&appname=rbamdemo&id=NC_000019&tracks=[key:sequence_track][key:alignment_track,display_name:Example1,dbname:cSRA,annots:http\://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh38/rnaseq/GRCh38.illumina.brain.1.bam,Layout:Adaptive,ShowAlnStat:true,GraphHeight:60]&assm_context=GCF_000001405.40"></a>
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</div>
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<p/>
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<h3>Example 2</h3>
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<p/>
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Homo sapiens: chromosome 22, assembly GRCh37.p13 (<a href="https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.25">https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.25</a>)<br>
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BAM file is hosted at http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqBjG1bAlnRep1.bam
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<div id="SViewer1" class="SeqViewerApp" data-autoload><a href="?embedded=full&appname=rbamdemo&id=NC_000022.10&tracks=[key:sequence_track][key:alignment_track,display_name:Example2,dbname:cSRA,annots:http\://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqBjG1bAlnRep1.bam,Layout:Adaptive,ShowAlnStat:true,GraphHeight:60]&v=33121080:33121170&assm_context=GCF_000001405.25"></a>
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</div>
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<p/>
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</div>
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</main>
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<div id="footer"></div>
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<script>
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$(document).ready(function(){
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$('#header').load("header.html");
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});
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</body>
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