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program [2012/12/12 10:34]
mbleda 		program [2017/05/24 14:25] (current)
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 +====== Day 1 ======
  
 +===== 11:00 – 11:30 Course presentation. =====
 +  *Joaquin Dopazo.
 +
 +===== 11:30 – 12:00 Introduction to Linux command line. =====
 +  *Pablo Escobar
 +{{:intro-linux-mda12.pdf|}}
 +
 +===== 12:00 – 13:00 Introduction to NGS technologies. =====
 +  *Javier Santoyo
 +{{:ngs_introduction_2012_12_10_valencia_mda12.pdf|NGS introduction slides}}
 +
 +===== 13:00 – 13:30 Computing infrastructure for NGS analyses. =====
 +  *Pablo Escobar.
 +{{:presentacion-it-ngs-valencia-mda12v2.pdf|}}
 +
 +=====13:30 – 15:00 Lunch break =====
 +//Will be held in the cafeteria of the CIPF.//
 +
 +===== 15:00 – 16:30 NGS data preprocessing concepts. =====
 +  *Jose Carbonell.
 +
 +Handling sequence files.
 +
 +Fasta and fastq file formats overview.
 +
 +Encoding quality metrics.
 +
 +Quality control tools.
 +
 +Bias detection.
 +
 +Sequence filtering.
 +
 +{{:sequence_preprocessing.pdf|}}
 +
 +
 +===== 16:30 – 17:00 Coffee break =====
 +//Will be held in the cafeteria of the CIPF.//
 +
 +
 +===== 17:00 – 18:30 NGS data preprocessing  practical session. =====
 +  *Jose Carbonell and Francisco Garcia.
 +
 +Hands on session with FastQC and FastX-Toolkit programs.
 +
 +{{::intro-linux-pescobar.pdf|}}
 +
 +{{:sesion_practica_sequencing.pdf|}}
 +
 +{{:sesion_practica_sequencing.odt|}}
 +
 +
 +===== 21:00 GALA DINNER =====
 +
 +  * See details here: {{:course_dinner.pdf|}}
 +
 +
 +
 +====== Day 2 ======
 +
 +=====10:00 – 11:30 Sequence alignment concepts. =====
 +  *Enrique Vidal.
 +
 +Reference genome as a concept.
 +
 +NGS alignment programs and algorithms.
 +
 +SAM/BAM and BED file formats overview.
 +
 +Mapped reads visualization.
 +
 +Quality control of the mapping.
 +
 +Local realignment.
 +
 +Computational needs.
 +
 +{{:mda12v2-alignment.pdf|}}
 +
 +=====11:30 – 12:00 Coffee break =====
 +//Will be held in the cafeteria of the CIPF.//
 +
 +
 +===== 12:00 – 13:30 Sequence alignment  practical session. =====
 +  *Enrique Vidal and David Montaner.
 +
 +Hands on session with alignment programs: bowtie, bwa and bfast.
 +
 +Overview of quality control and visualization tools: bamQC, GATK and IGV.
 +
 +Data handling with SAMtools.
 +
 +{{::mda-alignment_hands_on.pdf|}}
 +
 +[[align_handson | Alignment hands on ]] 
 +
 +
 +===== 13:30 – 15:00 Lunch break =====
 +//Will be held in the cafeteria of the CIPF.//
 +
 +
 +===== 15:00 – 16:30 Variant calling in NGS experiments; concepts. =====
 +  *Jorge Jimenez.
 +
 +Variant types: SNPs and InDels.
 +
 +Calling procedures and algorithms. 
 +
 +VCF file formats overview.
 +
 +Introduction to the programs GATK, Annovar and Variant. 
 +
 +Variant filtering.
 +
 +The problem of the missing data.
 +
 +Variant annotation.
 +
 +Data bases and data repositories: dbSNP and the 1000 genomes project.
 +
 +{{:variant_calling.pdf|}}
 +
 +
 +===== 16:30 – 17:00 Coffee Break =====
 +
 +
 +===== 17:00 – 18:30 Variant calling practical session. =====
 +  *Jorge Jimenez and Martina Marba.
 +
 +Hands on with GATK, Annovar and IGV.
 +
 +{{:variant_calling_practical.pdf|}}
 +
 +[[calling_handson | variant calling hands on ]]
 +
 +
 +====== Day 3 ======
 +
 +
 +===== 9:30 – 11:30 Results interpretation. =====
 +  *Jorge Jimenez and Enrique Vidal
 +
 +A general view on how to interpret BIER analysis pipeline and results. Some remarks on experiment design.
 +
 +{{:report.pdf|}}
 +
 +{{::mda-_remarks.pdf|}}
 +
 +
 +===== 11:30 – 12:00 Coffee break =====
 +//Will be held in the cafeteria of the CIPF.//
 +
 +
 +===== 12:00 – 14:00 Some CIPF tools for visualization, variant characterization and pathway analysis. =====
 +  *Patricia Sebastian and Marta Bleda
 +
 +Variant, CellBase, Genome Maps and Pathway analysis.
 +
 +{{:pathwayanalysis.pdf|}}
 +
 +{{::cipf_tools_marta_bleda.pdf|Some_CIPF_tools_presentation.pdf}}\\
 +{{::example_files.zip|example files}}