This material is linked to an online training. It is not intended to be followed via e-learning only because not all info is here.

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

Toy data sets for variant calling

The data sets of the variant analysis training. These are human paired-end data of the 1000 genomes project (sample ID: NA18507):

• the two files at the bottom consist of reads that map to chromosome 21
• the two files in the middle contain randomly picked 10% of the reads of the previous files (even smaller and therefore suited for mapping)
• the two files at the top contain randomly picked 1% of the reads of the two files with reads that map to chromosome 21.

These are small, workable files that were generated based on real DNASeq data.

Software for metagenomics

• Lotus2
• vegan

Software for bisulfite sequencing analysis

• Bismark