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 (Not for QuantSeq FWD library prep without UMIs)

• 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 (Not for QuantSeq FWD library prep without UMIs)

• Gene counting (FeatureCounts V1.6.4)

• Differential gene expression analysis (DESeq2 V1.18.1)

IMPORTANT: A minimum of three (3) biological replicates per condition is required to perform differential gene expression (DGE). If fewer than three replicates are provided, the DGE option in the parameters will be disabled and the analysis will not be executed.

NOTE: The QuantSeq REV pipeline does not include APA analysis (Alternative PolyAdenylation site).