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namespace:doc-mach:course-bioinfo2020 [2019/12/12 14:49]
mickey [Lecture 2. (120-min)] 		namespace:doc-mach:course-bioinfo2020 [2020/01/16 14:37] (current)
mickey
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 [[:​namespace:​doc-mach:​sandbox-course-bioinfo2020|Sandbox of '​Course of Genome Bioinformatics 2020'​]] [[:​namespace:​doc-mach:​sandbox-course-bioinfo2020|Sandbox of '​Course of Genome Bioinformatics 2020'​]]
  
-What computer will we use?+[[:​namespace:​doc-mach:​preparation-course-bioinfo2020|Preparation of '​Course of Genome Bioinformatics 2020'​]]
  
-  * Linux server+[[:​namespace:​doc-mach:​installed-software|List of software installed on soroban]]
  
-  * If personal computer, e.g. VirtualBox, to have the same organization of data, libraries, programs, etc. +[[:namespace:doc-mach:usage-soroban|Usage ​of 'soroban' ​server]]
- +
-Questions MK191010. +
- +
-  * Can we fix the number of participants?​ e.g. 15 or 20 +
- +
-  * Can we select simply those 15 who applies first? +
- +
-  * ask motivation letter? +
- +
-Lab work 5hr +
- +
-64hr +
- +
-8days x8hr +
- +
-Afternoon of 1st day +
- +
-7days +
- +
-Close at morning of the last day +
- +
-Room reservation,​ depend on the number of participants +
- +
-Windows computer at CMCC computer room +
- +
-====== Program / PROGRAMACIÓN ====== +
- +
-====== Day 1. ====== +
- +
-<font 20px/​Verdana,​ sans-serif;;#​000000;;​inherit>​**Program / PROGRAMACIÓN**</​font>​ +
- +
-<font 20px/​Verdana,​ sans-serif;;#​000000;;​yellow>​Day 1. Monday 6</​font> ​ <font inherit/​inherit;;​inherit;;#​ffcc00>​14:30</​font><​font inherit/​inherit;;​inherit;;​yellow>​hrs</​font><​font inherit/​Verdana,​ sans-serif;;#​000000;;​yellow>​KAWAI,​ FUJIYOSHI,</​font>​ <font inherit/​inherit;;​inherit;;​aqua>​(ABANTO?​)</​font>​ +
- +
-====== Lecture 1. ====== +
- +
-<font medium/​Verdana,​ sans-serif;;#​000000;;#​00ff99>​Lecture 1. (120-min)</​font>​ +
- +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​Brief review of introduction to Genomic, Metagenomic and Transcriptomic Analyses</​font>​ +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​Amplicon analysis</​font>​ +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​From single genes to genomics: genomics</​font>​ +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​From single genes to genomics: metagenomics/​metagenomic binning</​font>​ +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​From single genes to genomics: transcriptomics</​font>​ +
- +
- +
-===== Lecture 2. (120-min) ===== +
- +
-===== <font medium/​Verdana,​ sans-serif;;#​000000;;#​00ff66>​Lecture 2. (120-min)</​font>​ ===== +
-<font medium/​Verdana,​ sans-serif;;#​000000;;#​00ff66>​Lecture 2. (120-min)</​font>​ +
- +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​Statistical mind to find more concrete association with phenomena</​font>​ +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​What is your question / How to test your question / Importance of experimental design</​font>​ +
- +
-====== Day 2. ====== +
- +
-<font 20px/​Verdana,​ sans-serif;;#​000000;;#​ffff00>​Day 2. Tuesday 7 9:​00</​font> ​ <font inherit/​inherit;;​inherit;;​yellow>​ÁVILA</​font>​ +
- +
-<font medium/​Verdana,​ sans-serif;;#​000000;;#​00ff66>​Lecture 3. (90-min) AA</​font>​ +
- +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​Sequencers,​ sequencing platform (Illumina, long read)</​font>​ +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​Basic data format of basic sequence data (FASTA, GENBANK)</​font>​ +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​Basic data format ​of 'next-generation' ​sequence (NGS) data (FASTQ)</​font>​ +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​Quality information of positions of reads</​font>​ +
- +
-<font medium/​Verdana,​ sans-serif;;#​000000;;#​33ccff>​Lab session 1. (120-min)</​font>​ +
- +
-<font medium/​Verdana,​ sans-serif;;#​000000;;#​00ff66>​Lecture 4. 14:30 (90-min) AA</​font>​ +
- +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​Sequence alignment, sequence similarity search</​font>​ +
- +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​Two basic approaches, mapping and assembly</​font>​ +
- +
-<font medium/​Verdana,​ sans-serif;;#​000000;;#​33ccff>​Lab session 2. (120-min)</​font>​ +
- +
-====== Day 3. ====== +
- +
-<font 20px/​Verdana,​ sans-serif;;#​000000;;​yellow>​Day 3. Wednesday 8 9:00 KAWAI,</​font> ​ <font 20px/​inherit;;​inherit;;#​ffff00>​LARAMA</​font>​ +
- +
-<font inherit/​inherit;;​inherit;;​yellow>​MK will send previous material to Giovanni,</​font>​ +
- +
-<font inherit/​inherit;;​inherit;;​yellow>​Share documents</​font>​ +
- +
-<font medium/​Verdana,​ sans-serif;;#​000000;;​inherit>​Practice 1. (120-min) GL</​font>​ +
- +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​UNIX basic command, to sniff around sequence files (cd, pwd, ls etc.)</​font>​ +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​Examine file contents of MiSeq</​font>​ +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​File organization,​ concept of Path</​font>​ +
- +
-<font medium/​Verdana,​ sans-serif;;#​000000;;​inherit>​Practice 2. (120-min) GL</​font>​ +
- +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​Text processing (grep, less, tail, head,​..)</​font>​ +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​To get familiar with NGS sequences #1 (examine NGS sequence files)</​font>​ +
-  * <font 14.666666984558105px/​inherit;;​inherit;;​inherit>​Check contents of fastq</​font>​ +
- +
-<font medium/​Verdana,​ sans-serif;;#​000000;;​inherit>​Practice 3. (120-min) MK</​font>​ +
- +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​Text processing (wc, cut, sed, awk, redirect (> , >> ) etc.), gzip</​font>​ +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​To get familiar with NGS sequences #2 (sequential commands by pipe)</​font>​ +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​count how many of reads of fastq</​font>​ +
- +
-<font medium/​Verdana,​ sans-serif;;#​000000;;​inherit>​Practice 4. (120-min) MK</​font>​ +
- +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​Shell script (Batch processing)</​font>​ +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​Editor (vim)</​font>​ +
- +
-<font 20px/​Verdana,​ sans-serif;;#​000000;;​yellow>​Day 4. Thursday 9 9:00 KAWAI,</​font> ​ <font 20px/​Verdana,​ sans-serif;;#​000000;;#​ffff00>​LARAMA</​font>​ +
- +
-<font medium/​Verdana,​ sans-serif;;#​000000;;​inherit>​Practice 6. (120-min) GL</​font>​ +
- +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​R statistics and graphics language #​1</​font>​ +
- +
-<font medium/​Verdana,​ sans-serif;;#​000000;;​inherit>​Practice 7. (120-min) GL</​font>​ +
- +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​R statistics and graphics language #​2</​font>​ +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​Goal:</​font>​ * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​Do (small) analysis and make report of statistical test (apa format)</​font>​ +
- +
-<font medium/​Verdana,​ sans-serif;;#​000000;;#​33ccff>​Lab session 3. (240-min)</​font>​ +
- +
-<font 20px/​Verdana,​ sans-serif;;#​000000;;​yellow>​Day 5. Friday 10 9:00 KAWAI,</​font> ​ <font 20px/​inherit;;​inherit;;#​ffff00>​LARAMA</​font><​font inherit/​inherit;;​inherit;;​yellow>,​ ÁVILA</​font>​ +
- +
-<font medium/​Verdana,​ sans-serif;;#​000000;;​inherit>​Lecture 6. (120-min) GL</​font>​ +
- +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​Quality control of raw sequence data, basic tools for sequence and NGS data</​font>​ +
- +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​Commands for NGS analyses</​font>​ +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​Commands for sequence analyses</​font>​ +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​Brief review of online resources / web services</​font>​ +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​NGSToolkit (instead of FastQC)</​font>​ +
- +
-<font medium/​Verdana,​ sans-serif;;#​000000;;​inherit>​Practice 8. (120-min)</​font>​ +
- +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​To get familiar with NGS sequences #3 (</​font><​font inherit/​Verdana,​ sans-serif;;​inherit;;​inherit>​Shell script / make your own pipeline for custom</​font><​font inherit/​Verdana,​ sans-serif;;​inherit;;​inherit>​analysis</​font><​font inherit/​Verdana,​ sans-serif;;​inherit;;​inherit>​and record</​font><​font inherit/​Verdana,​ sans-serif;;​inherit;;​inherit>​of analysis / screen command)</​font>​* <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​Sequence similarity search against a genome at hand (Do BLAST search locally)</​font>​ +
- +
-<font 16px/​Verdana,​ sans-serif;;​inherit;;​inherit>​Lab XX (240-min)</​font>​ +
- +
-<font 20px/​Verdana,​ sans-serif;;#​000000;;​yellow>​Day 6. Monday 13 9:00 ÁVILA</​font> ​  , (<font inherit/​inherit;;​inherit;;#​ffff00>​LARAMA</​font>​) +
- +
-<font medium/​Verdana,​ sans-serif;;#​000000;;​inherit>​Lecture 7 and Practice 9. (240-min)</​font>​ +
- +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​Public sequence database</​font>​ +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​Local mirror of databases</​font>​ +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​Usage of information of public database</​font>​ +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​e.g. Mapping (bowtie2)</​font>​ +
- +
-<font medium/​Verdana,​ sans-serif;;#​000000;;​inherit>​Lecture 8 and Practice 10. (240-min)</​font>​ +
- +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​Genome assembly</​font>​ +
- +
-<font 20px/​Verdana,​ sans-serif;;#​000000;;​yellow>​Day 7. Tuesday 15 9:00 KAWAI → tuesday</​font>​ +
- +
-<font medium/​Verdana,​ sans-serif;;#​000000;;​inherit>​Lecture 9 and Practice 11. (120-min) MK</​font>​ +
- +
- \\ +
-* <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​Protein-coding gene prediction, RNA-coding gene prediction, gene annotation → MK</​font>​ +
- +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​Muliple sequence alignment</​font>​ +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​protein domain search</​font>​ +
- +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​Gene contents of genome</​font>​ +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​Concept of ortholog</​font>​ +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​Concept of conserved single-copy genes</​font>​ +
- +
-<font medium/​Verdana,​ sans-serif;;#​000000;;​inherit>​Lecture 10 and Practice 12. (120-min) MK</​font>​ +
- +
-<font medium/​Verdana,​ sans-serif;;#​000000;;​inherit>​Lecture 11 and Practice 13. (120-min) MK</​font>​ +
- +
-<font medium/​Verdana,​ sans-serif;;#​000000;;​inherit>​Lecture 12 and Practice 14. (120-min) MK</​font>​ +
- +
-<font 20px/​Verdana,​ sans-serif;;#​000000;;​yellow>​Day 8. Wednsday 16</​font> ​ <font inherit/​inherit;;​inherit;;#​ffcc33>​9:​00 - 13:​00</​font><​font inherit/​inherit;;​inherit;;​yellow>​ABANTO</​font>​ +
- +
-<font medium/​Verdana,​ sans-serif;;#​000000;;​inherit>​Lecture 10 and Practice 12. (180-min)</​font>​ +
- +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​Introduction of analyses</​font>​ +
- +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​Pangenome</​font>​ +
-  * <font 11pt/​Verdana,​ sans-serif;;​inherit;;​inherit>​Phylogenetic tree</​font>​ +
- +
-<font 20px/​Verdana,​ sans-serif;;#​000000;;#​ffff00>​Day 9. Thursday 17 9:00 KAWAI, LARAMA</​font>​ +
- +
-  * +
-  * Discuss plans +
-  * groups work +
-  * proposal +
-  * paper introducce +
-  * apply what they learned +
- +
-git, ask Raphel+
  
  
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  • Last modified: 2019/12/12 14:49
  • by mickey