How are my QuantSeq and LUTHOR HD data analyzed with Kangooroo?

The QuantSeq and LUTHOR HD data analysis pipelines include:

• MultiQC analysis of raw FASTQ files (multiqc V1.5)

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

• Trimming (Cutadapt V1.18)

• MultiQC analysis of trimmed FASTQ files (multiqc V1.5)

• Alignment (STAR V2.6.1a)

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

• UMI collapsing (if UMIs are introduced in the QuantSeq FWD library preps)

• Gene counting (FeatureCounts V1.6.4)

• Differential gene expression analysis (DESeq2 V1.18.1)