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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)

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