How are my WTS data analyzed with Kangooroo?

The WTS data analysis pipeline includes:

• MultiQC analysis of raw FASTQ files (multiqc V1.5)

• UMI extraction (if UMI option specified in the pipeline´s parameters)

• Trimming (Cutadapt V1.18)

• MultiQC analysis of trimmed FASTQ files (multiqc V1.5)

• Alignment (STAR V2.6.1a)

• UMI collapsing (If UMI option specified in the pipeline´s parameters)

• Coverage and MultiQC analysis of aligned files (multiqc V1.5)

• 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)

IMPORTANT: A minimum of three (3) biological replicates per condition is required to perform differential gene expression (DGE). If fewer than three replicates are provided, the DGE option in the parameters will be disabled and the analysis will not be executed.