Difference between revisions of "Hak-Min Kim KOREF"
From kogic.kr
| (5 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
| + | <p> </p> | ||
| + | |||
| + | <p> </p> | ||
| + | |||
<p><span style="font-size:20px"><strong>KOREF</strong></span></p> | <p><span style="font-size:20px"><strong>KOREF</strong></span></p> | ||
| − | <p><span style="font-size:16px">1. Raw data and project folder information</span></p> | + | <hr /> |
| + | <p> </p> | ||
| + | |||
| + | <p><strong><span style="font-size:16px">1. Raw data and project folder information</span></strong></p> | ||
<ol style="list-style-type:upper-alpha"> | <ol style="list-style-type:upper-alpha"> | ||
| Line 14: | Line 21: | ||
</ol> | </ol> | ||
| − | <p | + | <hr /> |
| + | <p> </p> | ||
| − | <p><span style="font-size:16px">2. Paper status: Published (</span><span style="font-size:16px"><a href="https://www.nature.com/articles/ncomms13637]">An ethnically relevant consensus Korean reference genome is a step towards personal reference genomes.</a> <em>Nature communications</em>, 2016)</span></p> | + | <p><span style="font-size:16px"><strong>2. Paper status</strong>: Published (</span><span style="font-size:16px"><a href="https://www.nature.com/articles/ncomms13637]">An ethnically relevant consensus Korean reference genome is a step towards personal reference genomes.</a> <em>Nature communications</em>, 2016)</span></p> |
| − | <p | + | <hr /> |
| + | <p> </p> | ||
| − | <p><span style="font-size:16px">3. Analysis result</span></p> | + | <p><strong><span style="font-size:16px">3. Analysis result</span></strong></p> |
<ol style="list-style-type:upper-alpha"> | <ol style="list-style-type:upper-alpha"> | ||
| Line 34: | Line 43: | ||
</ol> | </ol> | ||
| − | <p | + | <hr /> |
| + | <p> </p> | ||
| − | <p><span style="font-size:16px">4. Related script</span></p> | + | <p><strong><span style="font-size:16px">4. Related script</span></strong></p> |
<ol style="list-style-type:upper-alpha"> | <ol style="list-style-type:upper-alpha"> | ||
| Line 54: | Line 64: | ||
</ol> | </ol> | ||
| − | <p | + | <hr /> |
| + | <p> </p> | ||
| − | <p><span style="font-size:16px">5. Methods</span></p> | + | <p><strong><span style="font-size:16px">5. Methods</span></strong></p> |
<ol style="list-style-type:upper-alpha"> | <ol style="list-style-type:upper-alpha"> | ||
| + | <li>Assembly process<br /> | ||
| + | <br /> | ||
| + | <img alt="" src="/ckfinder/userfiles/images/5_KOREF_assembly_process.PNG" style="height:790px; width:700px" /><br /> | ||
| + | </li> | ||
<li><span style="font-size:16px">All methods are described in the method & material section of the published article.</span></li> | <li><span style="font-size:16px">All methods are described in the method & material section of the published article.</span></li> | ||
</ol> | </ol> | ||
Latest revision as of 12:08, 21 August 2019
KOREF
1. Raw data and project folder information
- Project folder:
- KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/
- KOREF서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/
- Raw data information: http://in.tgi.kr/index.php/Overall_Data_Information
2. Paper status: Published (An ethnically relevant consensus Korean reference genome is a step towards personal reference genomes. Nature communications, 2016)
3. Analysis result
- Assembly result: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Assembly
- Annotation result (Gene set / Repeat): KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Annotation
- Ethnic gene prediction result: KOREF서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/GenePrediction_for_All_assemblies_BestHit
- Ethnic repeat masking result: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Ethnic_RepeatMask
- Mitochondria assembly result: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Mitochondria_assembly
- Ethnic assemblies segmental duplication result: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/SegmentalDuplication
4. Related script
- Repeat maksing
- Run repeat masking: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Ethnic_RepeatMask/0_RepeatMasking_the_genome.pl
- Count the hetero variants in repeat region: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Ethnic_RepeatMask/1_Count_hetero_variants_in_repeat_region_withArray.pl
- Sspace_longread (scaffolding program)
- Run Sspace_longread with Pacbio and Moleculo data: KPGP서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/Assembly/3.Pacbio_Moleculo_SSPACE_with_2/script/0_SSPACE-longread_run_with_Pacbio_Moleculo.pl
- Exonerate unmapped count script: KOREF서버 /BiO/Research/Project1/TGI-KOREF-Genome-2013-06/GenePrediction_for_All_assemblies_BestHit/Exonerate_unmpped_count.pl
5. Methods
- Assembly process
- All methods are described in the method & material section of the published article.
