Workflow for Spliced RNAseq data
FastQC (Read Quality Control)
fastp (Read Trimming)
STAR (Read mapping)
featurecounts (transcript read counts)
kallisto (transcript [pseudo]counts)
Here we provide the tools to perform paired end or single read RNA-Seq analysis including raw data quality control, differential expression (DE) analysis and functional annotation. As input files you may use either zipped fastq-files (.fastq.gz) or mapped read data (.bam files). In case of paired end reads, corresponding fastq files should be named using .R1.fastq.gz and .R2.fastq.gz suffixes.
All analysis steps are illustrated in the pipeline