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UMI extraction (if UMIs are introduced in the library preps)
Trimming (Cutadapt V1.18)
FastQC analysis of trimmed FASTQ files (FASTQC V0.11.7)
Alignment (STAR V2.6.1a)
UMI collapsing (more info can be found here)
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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