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Reproducible genomic data analysis using short and long-read RNAseq data
Description of the workshop:
The purpose of the workshop is to introduce a framework for the processing of NGS datasets with a special focus on bioinformatics analysis of RNA-seq data. During the workshop attendees will get familiar with the current transcriptomic technologies producing short (Illumina) and long (PacBio) reads - their advantages, limitations and possible applications to monitor gene expression. This will be a combined tutorial and hands-on session. Attendees will be able to perform analysis themselves.
In the tutorial we will explain basic concepts of RNAseq technologies, features of the reference gene annotation, an overview of the available pipelines used in the consortium projects, such as ENCODE and Blueprint. Related to this, we will explain the problem of uniform and reproducible processing of large amount of NGS data. We will introduce the basic concepts of a framework for computational pipelines and will show how it can be used to simplify the writing of RNA-Seq pipelines in portable manner across different execution environments.
In the practical hands-on part we will describe how to write pipelines in a reproducible manner by using NextFlow - a pipeline management tool. Within the part of bioinformatic analysis we will explain common data formats (fastq, bam/sam, gtf, bed, bigWig), will show how to perform quality control of the transcriptomic data, read mapping, gene quantification and some downstream analysis. For the execution of the computational analysis we will use GRAPE, a Nextflow-based RNAseq pipeline environment. Within the pipeline, STAR will be used for aligning the RNAseq reads and creating the signal files and RSEM for producing isoform and gene quantifications, thus following the ENCODE3 production workflow for RNAseq data . The practical part will also include visualisation of the RNAseq signal in the UCSC genome browser.
Requirements: Basic linux knowledge (shell usage, basic commands) will be essential for understanding the hands-on content.
WEDNESDAY, 6 APRIL
|Introduction, data formats, reference genome annotation
|Computational pipelines, reproducibility and the Nextflow framework
|Short-read RNA-seq data processing with the GRAPE pipeline
|Data analysis, interpretation and visualization
|Iso-Seq™: Full-Length Transcript Analysis Using SMRT® Sequencing
Anna Vlasova 1,2
Paolo Di Tommaso 1,2
Emilio Palumbo 1,2
Julien Lagarde 1,2
Philip Lobb 3
1 Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
2 Universitat Pompeu Fabra (UPF), Barcelona, Spain
3 Field Bioinformatic Support, Europe, Pacific Biosciences