Difference between revisions of "Hak-Min Kim BOX"

From kogic.kr
(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...")
 
Line 1: Line 1:
−
<p><strong>Box jellyfish (Cubozoa) genome</strong></p>
+
<p><span style="font-size:20px"><strong>Box jellyfish (Cubozoa) genome</strong></span></p>
  
 
<hr />
 
<hr />
 
<p>&nbsp;</p>
 
<p>&nbsp;</p>
  
−
<p><strong>1. Raw data and project folder information</strong></p>
+
<p><span style="font-size:16px"><strong>1. Raw data and project folder information</strong></span></p>
  
 
<ol style="list-style-type:upper-alpha">
 
<ol style="list-style-type:upper-alpha">
−
<li>Project folder: Shark서버 /BiO/Research/Project1/TGI-BoxJellyfish-Genome-2018-07/</li>
+
<li><span style="font-size:16px">Project folder: Shark서버 /BiO/Research/Project1/TGI-BoxJellyfish-Genome-2018-07/</span></li>
−
<li>Raw data information:
+
<li><span style="font-size:16px">Raw data information:</span>
 
<ol style="list-style-type:lower-roman">
 
<ol style="list-style-type:lower-roman">
−
<li>Pacbio: /BiO/Research/Project1/TGI-BoxJellyfish-Genome-2018-07/0.Rawdata</li>
+
<li><span style="font-size:16px">Pacbio: /BiO/Research/Project1/TGI-BoxJellyfish-Genome-2018-07/0.Rawdata</span></li>
−
<li>Short reads: /BiO/Research/Project1/TGI-BoxJellyfish-Genome-2018-07/0.Rawdata/Genome/Sample_Cubic-jellyfish-161206</li>
+
<li><span style="font-size:16px">Short reads: /BiO/Research/Project1/TGI-BoxJellyfish-Genome-2018-07/0.Rawdata/Genome/Sample_Cubic-jellyfish-161206</span></li>
−
<li>RNA 2 tissue:
+
<li><span style="font-size:16px">RNA 2 tissue:</span>
 
<ol>
 
<ol>
−
<li>Medusa tissue: /BiO/Research/Project1/TGI-BoxJellyfish-Genome-2018-07/0.Rawdata/RNA/MedusaBell_20180601</li>
+
<li><span style="font-size:16px">Medusa tissue: /BiO/Research/Project1/TGI-BoxJellyfish-Genome-2018-07/0.Rawdata/RNA/MedusaBell_20180601</span></li>
−
<li>Tentacle tissue: /BiO/Research/Project1/TGI-BoxJellyfish-Genome-2018-07/0.Rawdata/RNA/Tentacle_20180611/1.RawData/Sample_TN1601R0105--GAGTGGAT</li>
+
<li><span style="font-size:16px">Tentacle tissue: /BiO/Research/Project1/TGI-BoxJellyfish-Genome-2018-07/0.Rawdata/RNA/Tentacle_20180611/1.RawData/Sample_TN1601R0105--GAGTGGAT</span></li>
 
</ol>
 
</ol>
 
</li>
 
</li>
Line 25: Line 25:
 
<p>&nbsp;</p>
 
<p>&nbsp;</p>
  
−
<p><strong>2. Paper status</strong>: Not yet published (Analysis in progress)</p>
+
<p><span style="font-size:16px"><strong>2. Paper status</strong>: Not yet published (Analysis in progress)</span></p>
  
 
<hr />
 
<hr />
 
<p>&nbsp;</p>
 
<p>&nbsp;</p>
  
−
<p><strong>3. Analysis result</strong></p>
+
<p><span style="font-size:16px"><strong>3. Analysis result</strong></span></p>
  
 
<ol style="list-style-type:upper-alpha">
 
<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><span style="font-size:16px">Genome size estimation result: Tiger서버 /BiO/Research/Project1/TGI-BoxJelly-Genome-2017-01/5.KmerAnalysis/TGI-BoxJelly-Genome-2017-01.K19.freq.stat</span></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
+
<li><span style="font-size:16px">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</span><br />
−
<table border="0" cellpadding="0" cellspacing="0" style="width:102.44%">
+
<br />
−
<tbody>
+
<img alt="" src="/ckfinder/userfiles/images/6_assembly_stat.PNG" style="height:306px; width:1055px" /><br />
−
<tr>
+
<br />
−
<td style="height:22px; width:26.0%">
+
<span style="font-size:16px">Due to the low depth PacBio raw data, PromethION long read sequencing was added and is currently being assembled by Hui-su Kim.</span></li>
−
<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>
 
</ol>

Revision as of 16:27, 20 August 2019

Box jellyfish (Cubozoa) genome

 

1. Raw data and project folder information

  1. Project folder: Shark서버 /BiO/Research/Project1/TGI-BoxJellyfish-Genome-2018-07/
  2. Raw data information:
    1. Pacbio: /BiO/Research/Project1/TGI-BoxJellyfish-Genome-2018-07/0.Rawdata
    2. Short reads: /BiO/Research/Project1/TGI-BoxJellyfish-Genome-2018-07/0.Rawdata/Genome/Sample_Cubic-jellyfish-161206
    3. RNA 2 tissue:
      1. Medusa tissue: /BiO/Research/Project1/TGI-BoxJellyfish-Genome-2018-07/0.Rawdata/RNA/MedusaBell_20180601
      2. Tentacle tissue: /BiO/Research/Project1/TGI-BoxJellyfish-Genome-2018-07/0.Rawdata/RNA/Tentacle_20180611/1.RawData/Sample_TN1601R0105--GAGTGGAT

 

2. Paper status: Not yet published (Analysis in progress)

 

3. Analysis result

  1. Genome size estimation result: Tiger서버 /BiO/Research/Project1/TGI-BoxJelly-Genome-2017-01/5.KmerAnalysis/TGI-BoxJelly-Genome-2017-01.K19.freq.stat
  2. 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



    Due to the low depth PacBio raw data, PromethION long read sequencing was added and is currently being assembled by Hui-su Kim.
Retrieved from "http://kogic.kr/index.php?title=Hak-Min_Kim_BOX&oldid=5384"