The CORALL data analysis pipeline includes:
UMI extraction
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)
Mix² for transcript isoform quantification (Mix² is a Lexogen´s proprietary software, for more information please visit our webpage Mix² RNA-Seq Data Analysis Software)
Gene counting (FeatureCounts V1.6.4)
Differential gene expression analysis (DESeq2 V1.18.1)