COURSE OVERVIEW
LOGISTICS
LAST COURSE PHOTOS
This shows you the differences between two versions of the page.
program [2013/03/15 03:52] jtarraga [16:30-18:00 HPG Aligner and sequence alignment libraries] |
program [2017/05/24 14:32] (current) |
||
---|---|---|---|
Line 1: | Line 1: | ||
+ | ;#; | ||
+ | <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 ==== | ||
+ | |||
+ | |||