Bulk RNASeq: from reads to counts
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
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.
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.
- RNA-seq assembly
- RNA-seq analysis for isoform detection
- RNA-seq analysis for detection of short RNA species
- fastQC
- trimmomatic
- Groomer
- STAR, Kallisto
- samtools
- Picard
- RSeQC
- HTSeq
Trainers
Janick Mathys
Guy Bottu
Guy Bottu is a bioinformatician at the VIB Bioinformatics Core in Ghent and the VIB Nucleomics Core in Leuven.
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
06 March 2020
Leuven - Park Inn by Radisson
Martelarenlaan 36
3010 Leuven
Belgium
06 March 2020
Leuven - Park Inn by Radisson
The hotel is located 300m from Leuven Central Station. The hotel connects to Leuven Central Station by a pedestrian bridge.
06 March 2020
Leuven - Park Inn by Radisson
Park Inn hotel has no own parking. It is possible to park underground in P1-Parking Station Leuven, Martelarenlaan 4, 3010 Leuven or in parking De Bond, Martelarenlaan 18, 3010 Leuven.
06 March 2020
Leuven - Park Inn by Radisson
+32 16 61 66 02
sales.leuven@parkinn.com