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The QuantSeq and LUTHOR HD data analysis pipelines include:

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

  • Trimming (Cutadapt V1.18)

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

  • Alignment (STAR V2.6.1a)

  • UMI collapsing

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

  • Gene counting (FeatureCounts V1.6.4)

  • Differential gene expression analysis (DESeq2 V1.18.1)

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