Bulk RNASeq: from reads to counts

advanced bioinformatics
omics
live training

Bulk RNASeq: from reads to counts

Target Audience:
All VIB staff
Location:

Park Inn, Leuven

General context

  • We perform quality control of the sequence reads to detect biases or contamination
  • We map the reads to the reference genome using a transcriptome model.
  • We perform a detailed QC analysis of the mapping results to detect potential problems.
  • The mapping results are used to obtain transcript counts 
Learning outcomes

During this training you will: execute a complete workflow at command line or in Galaxy or GenePattern to go from raw fastq files to count files.

Required skills

Familiarity with the Illumina sequencing process and with basic NGS data formats: FASTQ, SAM/BAM, GTF, ...If you do not meet these requirements you have to follow the "Introduction to the analysis of NGS data" training first. 

Experience with command line is required to do workflow in command line.

Not in the scope
  • RNA-seq assembly
  • RNA-seq analysis for isoform detection
  • RNA-seq analysis for detection of short RNA species
Software demonstrated
  • fastQC 
  • trimmomatic
  • Groomer 
  • STAR, Kallisto
  • samtools
  • Picard 
  • RSeQC
  • HTSeq

Trainers

Janick Mathys
VIB Training and Conferences, BE

Janick tries to help VIB scientists analyze their data by offering bioinformatics training and support. Next to organizing trainings, creating e-learning courses and teaching statistics, R, Python, Linux, HPC, bulk and single cell RNA-Seq analysis, she consults scientists and develops pipelines for omics analyses. Before joining VIB, she worked as a post-doc at KULeuven, doing research on transcriptomics and transcription regulation. She coordinated the Master of Bioinformatics program of KULeuven and taught the course on Biological Databases. 

ORCID
Contact Janick Mathys :
janick.mathys@vib.be

Program

9h30 - 15h00 Complete workflow from raw fastq files to count files in GenePattern or command line.

15h15 - 17h00 Automation of the workflow by creating a pipeline in GenePattern or running a bash script on command line

Practical info

Location & Venue

06 March 2020

Leuven - Park Inn by Radisson

Martelarenlaan 36
3010 Leuven
Belgium

Public transport

06 March 2020

Leuven - Park Inn by Radisson
Public transport

The hotel is located 300m from Leuven Central Station, just a short 5 minute walk.

Bike

06 March 2020

Leuven - Park Inn by Radisson
Bike

Bike parking Leuven

Using your bike for longer distances? Check Cycle Highways.

Route description

06 March 2020

Leuven - Park Inn by Radisson
Parking

Underground P1-Parking Station Leuven, Martelarenlaan 4, 3010 Leuven or parking De Bond, Martelarenlaan 18, 3010 Leuven.

Venue contact

06 March 2020

Leuven - Park Inn by Radisson
Location contact

+32 16 61 66 02

sales.leuven@parkinn.com