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Workflow

Filtering—Bowtie filters the input reads against abundant sequences, such as mitochondrial or ribosomal sequences, as defined by iGenomes at support.illumina.com/sequencing/sequencing_software/igenome.html.
Only sequences that do not align against abundant sequences are passed through to the next phase of the analysis. Bowtie filters read pairs when at least one read aligns to an abundant sequence. See Bowtie.
Alignment—The STAR aligner performs a spliced alignment of the filtered reads against the genome. Based on the user-specified genome, STAR aligns reads against known splice junctions. See Spliced Transcripts Alignment to a Reference (STAR).
Alignment to ERCC—If selected, STAR aligns all reads to the ERCC RNA spike-in sequences, independent of alignment to the transcriptome. The aligner counts reads that align to each spike-in sequence, calculates FPKMs, and computes the correlation between FPKMs and the expected spike-in concentrations.
Fusion Calling—If selected, the workflow uses STAR split-read alignment and Manta RNA-mode to call gene-fusions. See Manta (Gene Fusion Caller).
Variant Calling—The Strelka Variant Caller performs small variant calling. Strelka uses an RNA-specific random-forest-based variant scoring model, which was built using Platinum Genomes data as a reference. See Strelka.
Quantification—Salmon quantifies the expression of genes and transcripts defined in the reference annotation.