The QuantSeq and LUTHOR HD data analysis pipelines include:
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MultiQC analysis of raw FASTQ files (multiqc V1.5)
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UMI extraction*
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Trimming (Cutadapt V1.18)
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MultiQC analysis of trimmed FASTQ files (multiqc V1.5)
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Alignment (STAR V2.6.1a)
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MultiQC analysis of aligned files (multiqc V1.5)
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UMI collapsing*
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Gene counting (FeatureCounts V1.6.4)
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Differential gene expression analysis (DESeq2 V1.18.1)
*Not for Quantseq FWD with UMI and QuantSeq Rev libraries.
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).