How are my QuantSeq data analyzed?

The QuantSeq Data Analysis pipeline includes:

• FastQC analysis of raw FASTQ files (FASTQC V0.11.7)

• UMI extraction (if UMIs are introduced in the library preps)

• Trimming (Cutadapt V1.18)

• FastQC analysis of trimmed FASTQ files (FASTQC V0.11.7)

• Alignment (STAR V2.6.1a)

• MultiQC analysis of aligned files (multiqc V1.5)

• UMI collapsing (more info can be found here)

• Gene counting (FeatureCounts V1.6.4)

• Differential gene expression analysis (DESeq2 V1.18.1)