The course is intended for people who have short reads. Especially people with DNA-based reads are encouraged to follow this course and complete all the exercises.  For people with RNASeq data we organize a separate in-person course where we refer to specific topics from this e-learning. 

This course focuses on short reads and on the part of the workflow that is shared by most applications, going from quality control to visualization of the mapping results.

Please note that for applications using long reads we do have in-person courses that focus on genome assembly and variant analysis.

Exercises

• Belgian Galaxy server: you have to create a free account
• European Galaxy server: you have to create a free account

Data sets

• Arabidopsis control SE RNASeq sample (SRR074285.fastq.gz)
• Arabidopsis disease SE RNASeq sample (SRR074262.fastq.gz)
• shared raw Arabidopsis control SE RNASeq data on Galaxy
• shared groomed Arabidopsis control SE RNASeq data on Galaxy
• E. coli SE ChIP sample (SRR576933.fastq.gz)
• E. coli SE control sample (SRR576938.fastq.gz)
• human PE RNASeq sample, file 1 (SRR1039509_1.fastq.gz)
• human PE RNASeq sample, file 2 (SRR1039509_2.fastq.gz)

Tools used during this course

• Groomer
• FastQC
• Trimmomatic
• Bowtie
• BWA-MEM
• STAR
• HISAT2
• Kallisto
• Salmon
• PICARD
• samtools
• Qualimap
• RSeQC
• IGV

Links

• ASCII table to convert Phred scores into single characters
• FastQC manual
• Examples of good FastQC reports
• Explanation of the SAM/BAM file format
• Interpretation of SAM flags
• Overview of common NGS problems

Software for ChipSeq

• MACS3
• DeepTools
• RSAT peak-motifs

Software for variant calling

• GATK
• SnpEff & SnpSift

Software for metagenomics

• Lotus2
• vegan

Software for bisulfite sequencing analysis

• Bismark