EMBO High Throughput Sequencing Data Analysis, Cambridge, UK, 2014

EMBO High Throughput Sequencing Data Analysis, Cambridge, UK, 2014

Keywords

FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression, R-programming

Details

The material described here further corresponds to the 2nd and the 3rd Day of the course. They focus on:

pre-processing RNA-Seq data
manipulating the resulting files using R/Bioconductor
manipulating genic annotation using R/Bioconductor
extracting a count-table (at the gene level)
performing a gene differential expression analysis

Venue

  • EBI Campus, Welcome Trust Center, Hinxton, UK, 20-26th October 2014

Organisation

  • Organizer: Gabriella Rustici (@gabriella)
  • Trainers: Nicolas Delhomme (@delhomme), Bastian Schiffthaler (@bastian)

| Keywords | Details | Objectives | Content | Data |

Global learning objectives

  1. Introduction
  2. Quality Control
  3. Alignment
  4. Annotation
  5. Expression-estimation
  6. Differential-expression
    • What is a differential expression analysis
    • How to assess the quality (the biological meaningfulness) of the count data
    • What is a confounding factor
    • How to identify a confounding factor
    • How to block a confounding factor

| Keywords | Details | Objectives | Content | Data |

Content

  • EMBO October 2014 - Tutorial
  • EMBO October 2014 - Introduction
  • EMBO October 2014 - QC
  • EMBO October 2014 - Alignment
  • EMBO October 2014 - Annotation
  • EMBO October 2014 - Expression-estimate
  • EMBO October 2014 - Differential-expression

| Keywords | Details | Objectives | Content | Data |

Data

  • Uses the dataset Robinson, Delhomme et al., 2014

| Keywords | Details | Objectives | Content | Data |

Scientific topics: RNA-Seq

Keywords: FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression, R-programming

EMBO High Throughput Sequencing Data Analysis, Cambridge, UK, 2014 https://tess.elixir-europe.org/materials/embo-high-throughput-sequencing-data-analysis-cambridge-uk-2014 No description available RNA-Seq FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression, R-programming