How are my miRVEL data analyzed with Kangooroo?

The miRVEL Discovery and Profiling data analysis pipelines include:

• FASTQC analysis of raw FASTQ files (fastqc V012.1)

• Adapter Trimming (fastp V0.23.4)

• UMI deduplication (umicollapse-1.0.0 only for miRVEL Discovery Data)

• UMI Extraction (UMI-tools V1.1.6, only for miRVEL Discovery Data)

• Alignment (Bowtie V1.3.1)

• Mirtop Quantification (seqcluster V1.2.9 and mirtop V0.4.28)

• Genome quantification (Bowtie V1.3.1 and Samtools V1.21)

• 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.