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namespace:doc-mach:course-bioinfo2020 [2019/12/12 15:01] mickey [Program / PROGRAMACIÓN] |
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 | + | |
- | + | ||
- | ====== <fc #00ff00>//Program / PROGRAMACIÓN//</fc> ====== | + | |
- | + | ||
- | ====== 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 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 | + | |