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2 changes: 1 addition & 1 deletion 2022/03/22/omics_genome_submit/index.html
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Expand Up @@ -535,7 +535,7 @@ <h5 id="4-2-3-3-1-sample-stats-x2F-sample-val文件中报错ERROR"><a href="#4-2
</li>
<li><strong>SEQ_FEAT.TransLen</strong><ul>
<li>表示蛋白质长度与预测的蛋白质长度不匹配,运行错误</li>
<li>建议重跑table2asn,报错持续存在就写邮件把sample.sqn和运行的命令行发给NCBI(<a href="mailto:&#103;&#x65;&#x6e;&#111;&#x6d;&#x65;&#115;&#x40;&#x6e;&#x63;&#98;&#105;&#46;&#110;&#x6c;&#109;&#x2e;&#110;&#105;&#104;&#46;&#103;&#111;&#x76;">&#103;&#x65;&#x6e;&#111;&#x6d;&#x65;&#115;&#x40;&#x6e;&#x63;&#98;&#105;&#46;&#110;&#x6c;&#109;&#x2e;&#110;&#105;&#104;&#46;&#103;&#111;&#x76;</a>)让帮忙修改这个错误。</li>
<li>建议重跑table2asn,报错持续存在就写邮件把sample.sqn和运行的命令行发给NCBI(<a href="mailto:&#x67;&#x65;&#110;&#x6f;&#x6d;&#101;&#x73;&#64;&#x6e;&#x63;&#98;&#105;&#x2e;&#x6e;&#x6c;&#109;&#46;&#110;&#x69;&#104;&#x2e;&#103;&#111;&#x76;">&#x67;&#x65;&#110;&#x6f;&#x6d;&#101;&#x73;&#64;&#x6e;&#x63;&#98;&#105;&#x2e;&#x6e;&#x6c;&#109;&#46;&#110;&#x69;&#104;&#x2e;&#103;&#111;&#x76;</a>)让帮忙修改这个错误。</li>
</ul>
</li>
<li><strong>SEQ_FEAT.BadInternalCharacter</strong><ul>
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4 changes: 2 additions & 2 deletions 2022/05/27/omics_genome.survey_03.jellyfish/index.html
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Expand Up @@ -463,8 +463,8 @@ <h1 id="6-references"><a href="#6-references" class="headerlink" title="6. refer
<i class="fa fa-chevron-left"></i> 用k-mer分析进行基因组调查:(一)基本原理
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14 changes: 4 additions & 10 deletions 2024/06/22/omics_genome.assembly_TGS_Hifiasm_04.operate/index.html
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Expand Down Expand Up @@ -243,16 +243,10 @@ <h1 class="post-title" itemprop="name headline">
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<time title="Created: 2024-06-22 00:00:00" itemprop="dateCreated datePublished" datetime="2024-06-22T00:00:00+08:00">2024-06-22</time>
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Expand Down Expand Up @@ -539,7 +533,7 @@ <h1 id="4-log文件解释(debug)"><a href="#4-log文件解释(debug)" cl
</ol>
<ul>
<li>log文件会在打印完k-mer plot后,打印一行:<code>[M::purge_dups] homozygous read coverage threshold: 90.</code> </li>
<li>这个90是hifiasm确定的纯合子覆盖度值(用Ho_coverage代表)。要检查Ho_coverage值是否接近k-mer plot中确定的纯和峰值Ho_peak值,如果不接近(比如更接近He_peak值)那表明hifiasm错误地确定了纯合子覆盖度值,此时组装的基因组要么太大,要么太小。要用–homo-cov参数设置纯合子覆盖度值为Ho_peak值。</li>
<li>这个90是hifiasm确定的纯合子覆盖度值(用Ho_coverage代表)。要检查Ho_coverage值是否接近k-mer plot中确定的纯合峰值Ho_peak值,如果不接近(比如更接近He_peak值)那表明hifiasm错误地确定了纯合子覆盖度值,此时组装的基因组要么太大,要么太小。要用–homo-cov参数设置纯合子覆盖度值为Ho_peak值。</li>
</ul>
<ol start="3">
<li>纯合&#x2F;杂合碱基数量(number of het&#x2F;hom bases)</li>
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2 changes: 1 addition & 1 deletion about/index.html
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Expand Up @@ -246,7 +246,7 @@ <h1 class="post-title" itemprop="name headline">关于生信技工
<li>教育经历:目前(中山大学在职博士后,植物基因组进化),博士(中山大学,植物基因组进化),硕士(四川大学,植物进化),本科(西南大学,食品科学)。</li>
<li>微信公众号:生信技工</li>
<li>个人网站:<a target="_blank" rel="noopener" href="https://yanzhongsino.github.io/">https://yanzhongsino.github.io/</a></li>
<li>邮箱​:<a href="mailto:&#x79;&#97;&#110;&#46;&#x7a;&#x68;&#111;&#x6e;&#103;&#x2e;&#x73;&#x69;&#110;&#x6f;&#x40;&#x67;&#109;&#97;&#x69;&#x6c;&#46;&#x63;&#111;&#x6d;">&#x79;&#97;&#110;&#46;&#x7a;&#x68;&#111;&#x6e;&#103;&#x2e;&#x73;&#x69;&#110;&#x6f;&#x40;&#x67;&#109;&#97;&#x69;&#x6c;&#46;&#x63;&#111;&#x6d;</a></li>
<li>邮箱​:<a href="mailto:&#x79;&#x61;&#x6e;&#46;&#x7a;&#104;&#x6f;&#x6e;&#x67;&#x2e;&#115;&#x69;&#x6e;&#x6f;&#x40;&#x67;&#109;&#97;&#105;&#108;&#46;&#x63;&#x6f;&#109;">&#x79;&#x61;&#x6e;&#46;&#x7a;&#104;&#x6f;&#x6e;&#x67;&#x2e;&#115;&#x69;&#x6e;&#x6f;&#x40;&#x67;&#109;&#97;&#105;&#108;&#46;&#x63;&#x6f;&#109;</a></li>
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<hr>
<ul>
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8 changes: 4 additions & 4 deletions archives/2022/06/index.html
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Expand Up @@ -336,8 +336,8 @@ <h1 class="site-title">生信技工</h1>
</div>

<div class="post-title">
<a class="post-title-link" href="/2022/06/05/omics_genome.survey_04.KMC/" itemprop="url">
<span itemprop="name">用k-mer分析进行基因组调查:(四)用KMC进行k-mer频数统计</span>
<a class="post-title-link" href="/2022/06/05/omics_genome.survey_05.GenomeScope/" itemprop="url">
<span itemprop="name">用k-mer分析进行基因组调查:(五)用GenomeScope评估基因组特征</span>
</a>
</div>

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<div class="post-title">
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<span itemprop="name">用k-mer分析进行基因组调查:(五)用GenomeScope评估基因组特征</span>
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<span itemprop="name">用k-mer分析进行基因组调查:(四)用KMC进行k-mer频数统计</span>
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4 changes: 2 additions & 2 deletions archives/2022/page/3/index.html
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Expand Up @@ -416,8 +416,8 @@ <h1 class="site-title">生信技工</h1>
</div>

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<span itemprop="name">用k-mer分析进行基因组调查:(四)用KMC进行k-mer频数统计</span>
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<span itemprop="name">用k-mer分析进行基因组调查:(五)用GenomeScope评估基因组特征</span>
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4 changes: 2 additions & 2 deletions archives/2022/page/4/index.html
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</div>

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<a class="post-title-link" href="/2022/06/05/omics_genome.survey_05.GenomeScope/" itemprop="url">
<span itemprop="name">用k-mer分析进行基因组调查:(五)用GenomeScope评估基因组特征</span>
<a class="post-title-link" href="/2022/06/05/omics_genome.survey_04.KMC/" itemprop="url">
<span itemprop="name">用k-mer分析进行基因组调查:(四)用KMC进行k-mer频数统计</span>
</a>
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</div>

<div class="post-title">
<a class="post-title-link" href="/2022/06/05/omics_genome.survey_04.KMC/" itemprop="url">
<span itemprop="name">用k-mer分析进行基因组调查:(四)用KMC进行k-mer频数统计</span>
<a class="post-title-link" href="/2022/06/05/omics_genome.survey_05.GenomeScope/" itemprop="url">
<span itemprop="name">用k-mer分析进行基因组调查:(五)用GenomeScope评估基因组特征</span>
</a>
</div>

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</div>

<div class="post-title">
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<span itemprop="name">用k-mer分析进行基因组调查:(五)用GenomeScope评估基因组特征</span>
<a class="post-title-link" href="/2022/06/05/omics_genome.survey_04.KMC/" itemprop="url">
<span itemprop="name">用k-mer分析进行基因组调查:(四)用KMC进行k-mer频数统计</span>
</a>
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4 changes: 2 additions & 2 deletions atom.xml
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<link href="http://example.com/atom.xml" rel="self"/>

<link href="http://example.com/"/>
<updated>2024-06-21T03:01:31.919Z</updated>
<updated>2024-06-22T02:56:38.824Z</updated>
<id>http://example.com/</id>

<author>
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<link href="http://example.com/2024/06/22/omics_genome.assembly_TGS_Hifiasm_04.operate/"/>
<id>http://example.com/2024/06/22/omics_genome.assembly_TGS_Hifiasm_04.operate/</id>
<published>2024-06-21T16:00:00.000Z</published>
<updated>2024-06-21T03:01:31.919Z</updated>
<updated>2024-06-22T02:56:38.824Z</updated>


<summary type="html">基于三代HiFi reads用软件Hifiasm进行基因组的从头组装的详细讲解。</summary>
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8 changes: 4 additions & 4 deletions categories/omics/genome/genome-survey/index.html
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<span itemprop="name">用k-mer分析进行基因组调查:(四)用KMC进行k-mer频数统计</span>
<a class="post-title-link" href="/2022/06/05/omics_genome.survey_05.GenomeScope/" itemprop="url">
<span itemprop="name">用k-mer分析进行基因组调查:(五)用GenomeScope评估基因组特征</span>
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<a class="post-title-link" href="/2022/06/05/omics_genome.survey_05.GenomeScope/" itemprop="url">
<span itemprop="name">用k-mer分析进行基因组调查:(五)用GenomeScope评估基因组特征</span>
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<span itemprop="name">用k-mer分析进行基因组调查:(四)用KMC进行k-mer频数统计</span>
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<span itemprop="name">用k-mer分析进行基因组调查:(五)用GenomeScope评估基因组特征</span>
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<span itemprop="name">用k-mer分析进行基因组调查:(五)用GenomeScope评估基因组特征</span>
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<span itemprop="name">用k-mer分析进行基因组调查:(四)用KMC进行k-mer频数统计</span>
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<a class="post-title-link" href="/2022/06/05/omics_genome.survey_04.KMC/" itemprop="url">
<span itemprop="name">用k-mer分析进行基因组调查:(四)用KMC进行k-mer频数统计</span>
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<span itemprop="name">用k-mer分析进行基因组调查:(五)用GenomeScope评估基因组特征</span>
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<span itemprop="name">用k-mer分析进行基因组调查:(五)用GenomeScope评估基因组特征</span>
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<span itemprop="name">用k-mer分析进行基因组调查:(四)用KMC进行k-mer频数统计</span>
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<time title="Modified: 2024-06-21 11:01:31" itemprop="dateModified" datetime="2024-06-21T11:01:31+08:00">2024-06-21</time>
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