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Hak-Min Kim BOX

5,582 bytes added, 16:24, 20 August 2019
Created page with "<p><strong>Box jellyfish (Cubozoa) genome</strong></p> <hr /> <p> </p> <p><strong>1. Raw data and project folder information</strong></p> <ol style="list-style-type:upper..."
<p><strong>Box jellyfish (Cubozoa) genome</strong></p>

<hr />
<p>&nbsp;</p>

<p><strong>1. Raw data and project folder information</strong></p>

<ol style="list-style-type:upper-alpha">
<li>Project folder: Shark서버 /BiO/Research/Project1/TGI-BoxJellyfish-Genome-2018-07/</li>
<li>Raw data information:
<ol style="list-style-type:lower-roman">
<li>Pacbio: /BiO/Research/Project1/TGI-BoxJellyfish-Genome-2018-07/0.Rawdata</li>
<li>Short reads: /BiO/Research/Project1/TGI-BoxJellyfish-Genome-2018-07/0.Rawdata/Genome/Sample_Cubic-jellyfish-161206</li>
<li>RNA 2 tissue:
<ol>
<li>Medusa tissue: /BiO/Research/Project1/TGI-BoxJellyfish-Genome-2018-07/0.Rawdata/RNA/MedusaBell_20180601</li>
<li>Tentacle tissue: /BiO/Research/Project1/TGI-BoxJellyfish-Genome-2018-07/0.Rawdata/RNA/Tentacle_20180611/1.RawData/Sample_TN1601R0105--GAGTGGAT</li>
</ol>
</li>
</ol>
</li>
</ol>

<hr />
<p>&nbsp;</p>

<p><strong>2. Paper status</strong>: Not yet published (Analysis in progress)</p>

<hr />
<p>&nbsp;</p>

<p><strong>3. Analysis result</strong></p>

<ol style="list-style-type:upper-alpha">
<li>Genome size estimation result: Tiger서버 /BiO/Research/Project1/TGI-BoxJelly-Genome-2017-01/5.KmerAnalysis/TGI-BoxJelly-Genome-2017-01.K19.freq.stat</li>
<li>Assembly result: Orchid서버 /BiO/Research/Project1/TGI-BoxJellyfish-Genome-2018-07/1.Pacbio_Falcon_NonFilter/11K_11K/2-asm-falcon_11K_13K/p_ctg.fa
<table border="0" cellpadding="0" cellspacing="0" style="width:102.44%">
<tbody>
<tr>
<td style="height:22px; width:26.0%">
<p><strong>Read correction cutoff</strong></p>
</td>
<td colspan="5" style="height:22px; width:74.0%">
<p><strong>11K</strong></p>
</td>
</tr>
<tr>
<td style="height:22px; width:26.0%">
<p><strong>Assembly used read cutoff</strong></p>
</td>
<td style="height:22px; width:15.2%">
<p><strong>11K</strong></p>
</td>
<td style="height:22px; width:15.2%">
<p><strong>12K</strong></p>
</td>
<td style="height:22px; width:15.2%">
<p><strong>13K</strong></p>
</td>
<td style="height:22px; width:14.18%">
<p><strong>14K</strong></p>
</td>
<td style="height:22px; width:14.18%">
<p><strong>15K</strong></p>
</td>
</tr>
<tr>
<td style="height:21px; width:26.0%">
<p># of sequences</p>
</td>
<td style="height:21px; width:15.2%">
<p>10240 ea</p>
</td>
<td style="height:21px; width:15.2%">
<p>9396 ea</p>
</td>
<td style="height:21px; width:15.2%">
<p>8587 ea</p>
</td>
<td style="height:21px; width:14.18%">
<p>7594 ea</p>
</td>
<td style="height:21px; width:14.18%">
<p>6786 ea</p>
</td>
</tr>
<tr>
<td style="height:21px; width:26.0%">
<p>Total bases</p>
</td>
<td style="height:21px; width:15.2%">
<p>1284987375 bp</p>
</td>
<td style="height:21px; width:15.2%">
<p>1166025763 bp</p>
</td>
<td style="height:21px; width:15.2%">
<p>1045513771 bp</p>
</td>
<td style="height:21px; width:14.18%">
<p>909583732 bp</p>
</td>
<td style="height:21px; width:14.18%">
<p>775344685 bp</p>
</td>
</tr>
<tr>
<td style="height:21px; width:26.0%">
<p>Longest length</p>
</td>
<td style="height:21px; width:15.2%">
<p>1333152 bp</p>
</td>
<td style="height:21px; width:15.2%">
<p>997040 bp</p>
</td>
<td style="height:21px; width:15.2%">
<p>1183633 bp</p>
</td>
<td style="height:21px; width:14.18%">
<p>1116149 bp</p>
</td>
<td style="height:21px; width:14.18%">
<p>960575 bp</p>
</td>
</tr>
<tr>
<td style="height:21px; width:26.0%">
<p>Shortest length</p>
</td>
<td style="height:21px; width:15.2%">
<p>11522 bp</p>
</td>
<td style="height:21px; width:15.2%">
<p>12380 bp</p>
</td>
<td style="height:21px; width:15.2%">
<p>13566 bp</p>
</td>
<td style="height:21px; width:14.18%">
<p>14660 bp</p>
</td>
<td style="height:21px; width:14.18%">
<p>15238 bp</p>
</td>
</tr>
<tr>
<td style="height:21px; width:26.0%">
<p><strong>N50</strong></p>
</td>
<td style="height:21px; width:15.2%">
<p><strong>183,372</strong></p>
</td>
<td style="height:21px; width:15.2%">
<p><strong>181,743</strong></p>
</td>
<td style="height:21px; width:15.2%">
<p><strong>177,304</strong></p>
</td>
<td style="height:21px; width:14.18%">
<p><strong>172,930</strong></p>
</td>
<td style="height:21px; width:14.18%">
<p><strong>161,564</strong></p>
</td>
</tr>
<tr>
<td style="height:21px; width:26.0%">
<p>GC contents</p>
</td>
<td style="height:21px; width:15.2%">
<p>39.07%</p>
</td>
<td style="height:21px; width:15.2%">
<p>39.07%</p>
</td>
<td style="height:21px; width:15.2%">
<p>39.08%</p>
</td>
<td style="height:21px; width:14.18%">
<p>39.07%</p>
</td>
<td style="height:21px; width:14.18%">
<p>39.07%</p>
</td>
</tr>
<tr>
<td style="height:22px; width:26.0%">
<p>N bases (gaps)</p>
</td>
<td style="height:22px; width:15.2%">
<p>0.00%</p>
</td>
<td style="height:22px; width:15.2%">
<p>0.00%</p>
</td>
<td style="height:22px; width:15.2%">
<p>0.00%</p>
</td>
<td style="height:22px; width:14.18%">
<p>0.00%</p>
</td>
<td style="height:22px; width:14.18%">
<p>0.00%</p>
</td>
</tr>
</tbody>
</table>
</li>
</ol>
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