The QuantSeq and LUTHOR HD data analysis pipeline includes:
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)