Will be held in the cafeteria of the CIPF.
Handling sequence files.
Fasta and fastq file formats overview.
Encoding quality metrics.
Quality control tools.
Bias detection.
Sequence filtering.
Will be held in the cafeteria of the CIPF.
Hands on session with FastQC and FastX-Toolkit programs.
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.
Will be held in the cafeteria of the CIPF.
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.
Will be held in the cafeteria of the CIPF.
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.
Hands on with GATK, Annovar and IGV.
A general view on how to interpret BIER analysis pipeline and results. Some remarks on experiment design.
Will be held in the cafeteria of the CIPF.
Variant, CellBase, Genome Maps and Pathway analysis.