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title: "RNA-Seq Course Sevilla"
canonical: "https://help.biobam.com/space/BTP/618594318/RNA-Seq%20Course%20Sevilla"
format: markdown
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Details:  Title: RNA-Seq Data Analysis Workshop for Non-Model Organisms Date : 27.32. -29.3.2019 (3 days, 15 hours) Location : Sevilla, Spain Teachers : 2 Bioinformatics Experts from BioBam Bioinformatics S.L., Valencia, Spain Language:  Presentations in Spanish, Course material in English Target Audience (24 max.):  Biologists with no or little experience in analyzing RNA-Seq data.  Scope : Complete bioinformatics workflow of a de-novo transcriptomics data analysis will we covered in a 3 day workshop with theoretical (~60%) as well as practical hands on sessions (~40%). We will start with raw reads and discuss all steps until the biological interpretation of functional analysis results. The workshop design takes into consideration that we are treating with non-model organisms were no or little information exists in public databases. We will discuss up-to-date bioinformatics software solutions and provides hints about its execution including parameter setting, common pitfalls as well as input, output and system requirements. Day 1 Theory: 3 hours (9-12) Course presentation Introduction to sequencing technologies, RNA-Seq and de-novo transcriptomics for non-model organisms Introduction bioinformatics file formats (e.g. FASTA, FASTQ, BAM, VCF) and Blast2GO Preprocessing of raw reads: quality control (FastQC), adapter clipping, quality trimming Hands-On: 2 hours (12-14) Introduction to basic bioinformatics tools that will be used throughout the course including basic notions of the command line as well as an introduction to the Blast2GO user interface. Hands-on with a first set of FastQ files to perform its preprocessing including quality assessment and control. Summary of the day, group foto, discussion and questions. Day 2 Theory: 3 hours (9-12) RNA-Seq de-novo assembly (Trinity). Understand analysis outputs, statistics and its visualization. Functional annotation of novel genomes (Blast2GO Methodology) Hands-On: 2 hours (12-14) The pre-processed datasets obtained during the day of the workshop will be used to assemble the transcriptome. Transcripts will be filtered, quality assessed and functionally annotated with Gene Ontology terms. Summary of the day, discussion and questions. Day 3 Theory: 3 hours (9-12) Read Mapping (STAR and Bowtie2) and read expression quantification (Rsem, HTseq) Statistical Analysis of differential gene/isoform expression, pairwise and timeCourse) (EdgeR, MaSigPro) Functional analysis via Enrichment Analysis (Fisher's and GSEA) Hands-On: 2 hours (12-14) We will be assessing the differential expression profiles a multiple example datasets with different analysis strategies depending on the different experimental designs and biological questions. Results will be combined with the functional annotations created the previous day via different enrichment analysis methods. We will explore various visualization strategies to better understand and communicate the biological meaning of the obtained results. Workshop summary and closure, course evaluation, discussion and questions. Calendario  12.2. Reparto de Temario 19.2. Repaso Temario y diapositivas y definicion de ejercicios 26. 2. Repaso ejercicios, Revision Slides 5.3 Ensayo Dia 1 y 2 12.3 Ensayo Dia 2 y 3 21 y/o 25 Ajustes finales