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program [2013/03/15 03:52]
jtarraga [16:30-18:00 HPG Aligner and sequence alignment libraries]
program [2017/05/24 14:32] (current)
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 +;#;
 +<fs xx-large>Course Program</fs>
 +;#;
 +
 +====== User's session ======
 +
 +===== Monday =====
 +
 +==== 14:30-15:00 Registration ====
 +  
 +==== 15:00-15:30 Course reception ====
 +==== 15:30-16:00 Course Overview === 
 +  
 +
 +==== 16:30-17:00 Introduction to Linux Systems === 
 +//Pablo Escobar// \\
 +{{:intro-linux-mda13.pdf|}}
 +==== 17:00-18:00 Introduction to NGS Technologies for Variation Studies ====
 +//Javier Santoyo//  -  {{ngs_introduction_2013_03_11_valencia_mda13.pdf|Introduction to NGS technologies}}
 +\\
 +Youtube videos:
 +  *[[https://www.youtube.com/watch?v=HtuUFUnYB9Y| Illumina]]
 +  *[[https://www.youtube.com/watch?v=nlvyF8bFDwM | Solid]]
 +  *[[https://www.youtube.com/watch?v=bFNjxKHP8Jc] | FLX 454]]
 +===== Tuesday =====
 +
 +==== 09:30-11:00 Quality Control for NGS Raw Data  ====
 +//Francisco García//  - {{:mda13:qc_talk.pdf|Quality Control}}, {{:mda13:practical_session_with_solutions.pdf|practical session with solutions}}, {{:code.txt|}}.
 +
 +__Software__: FastQC, Fastx-Toolkit, HPC fastq
 +
 +__File formats__: fasta, fastq
 +
 +==== 11:30-13:00 Mapping NGS Reads for Genomic Studies ====
 +//Ignacio Medina//
 +
 +__Software__: HPG aligner, BWA, Bowtie2, SAMtools
 +
 +__File formats__: FASTQ, SAM/BAM
 +
 +{{:ngs-read-mapping-imedina-mda13.odp|}}    {{:ngs-read-mapping-imedina-mda13.pdf|}}
 +
 +Human reference chromosome 20 and paired-end dataset from chromosome 20 available at: http://www.opencb.org/projects/hpg/doku.php?id=aligner:getting_started
 +
 +==== 13:00-14:30 Lunch ====
 +Will be held in the cafeteria of the [[CIPF]].
 +
 +
 +==== 14:30-16:00 Quality control for Mapping === 
 +//Francisco Javier López//
 +
 +__Software__: QualiMap
 +
 +{{:mda13:map_qc.pdf|}}
 +
 +{{:mda13:igv.pdf|}}
 +
 +==== 16:30:18:00 Visualization of mapped reads ====
 +//Francisco Javier López//
 +  
 +__Software__: BAM viewer, IGV
 +
 +
 +==== 21:00 Gala Dinner ====
 +See [[gala_dinner|details]].
 +
 +
 +===== Wednesday =====
 +
 +==== 09:30-11:00 Variant Calling SNPs === 
 +//Jorge Jiménez//
 +  
 +__Software__: GATK
 +
 +__File formats__: VCF
 +
 +{{:variant_calling.pdf|}}
 +
 +[[ program:variant_handson | Variant calling hands on ]]
 +
 +==== 11:30-13:00 Variant Calling IN-DELS ====
 +//Jorge Jiménez//
 +
 +__Software__: GATK
 +
 +__File formats__: VCF
 +==== 13:00-14:30 Lunch ====
 +Will be held in the cafeteria of the [[CIPF]].
 +
 +
 +==== 14:30-16:00 Variant Annotation ====
 +//Marta Bleda//
 +  
 +__Software__: HPG variant effect
 +
 +PRESENTATION PDF: **{{:mda13:mbleda-mda13-variant_annotation.pdf|}}**
 +
 +PRESENTATION ODP: **{{:mda13:mbleda-mda13-variant_annotation.odp|}}**
 +
 +Example VCF: **{{:mda13:chb.exon.2010_03.sites.vcf.zip|}}**
 +==== 16:30:18:00 Association Studies ====
 +//Ignacio Medina, Cristina Yenyxe, Marta Bleda//
 +  
 +__Software__: HPG Variant
 +
 +__File formats__: VCF, ped
 +
 +{{:gwas-mda-13.odp|}}  {{:gwas-mda-13.pdf|}}
 +===== Thursday =====
 +
 +==== 09:30-11:00 Biological Data Bases === 
 +//Ignacio Medina//  
 +
 +{{:cellbase-imedina-mda13.odp|}}    {{:cellbase-imedina-mda13.pdf|}}
 +
 +Exercise file: **{{:mda13:gene_list.txt|}}**
 +
 + 
 +==== 11:30-13:00 Gene-Set Methodologies for NGS Data ====
 +//David Montaner//    
 +
 +{{:mda13:gene_set_ngs.odp|}}
 +
 +{{:mda13:gene_set_ngs.pdf|}}
 +
 +{{:mda13:gene_set_ngs.txt|}}
 +==== 13:00-14:30 Lunch ====
 +Will be held in the cafeteria of the [[CIPF]].
 +
 +
 +====== Developer's session ======
 +===== Thursday =====
 +
 +
 +==== 14:30-16:00 Introduction to software libraries and technologies ====
 +//Ignacio Medina//  
 +
 +{{:dev-intro-imedina-mda13.odp|}}    {{:dev-intro-imedina-mda13.pdf|}}
 +
 +==== 16:30-18:00 HPG Aligner and sequence alignment libraries====
 +//Joaquín Tárraga//  
 +
 +{{:mda13:hpg-aligner-jtarraga-mda13.pdf|}} {{:mda13:hpg-aligner-jtarraga-mda13.odp|}}
 +===== Friday =====
 +
 +==== 09:30-11:00 HPG Variant architecture and libraries === 
 +//Cristina Yenyxe//    
 +
 +{{:mda13:hpg-variant-developers.pdf|}}
 +==== 11:30-13:00 HTML5 visualization: Genome Maps and CellBrowswer ====
 +//Francisco Salavert// 
 + 
 +==== 13:00-14:30 Lunch ====
 +Will be held in the cafeteria of the [[CIPF]].
 +
 +
 +==== 14:30:16:00 Closing ====
 +
 + 
  
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