The QuantSeq and LUTHOR HD data analysis pipeline includes: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)
FastQC MultiQC analysis of trimmed FASTQ files (FASTQC V0.11.7multiqc V1.5)
Alignment (STAR V2.6.1a)
UMI collapsing (more info can be found here)
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)
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