Routes

Routes are the different analysis workflows.

Basic routes

Generic routes are sample-centric where the same analysis is performed independently for each sample. The available routes:

• rna-star: RNA-seq using STAR. Generates BAMs, normalized bigWigs, counts matrix, and various QC metrics.
• rna-salmon: RNA-seq using Salmon. Generates TPM/counts matrix and various QC metrics.
• rna-rsem: RNA-seq using RSEM. Generates FPKM/TPM/counts matrix and various QC metrics.
• rna-snv: RNA-seq variant detection. Generates BAMs, VCFs, and various QC metrics.
• chip: ChIP-seq. Generates BAMs, bigWigs, peaks, and various QC metrics.
• atac: ATAC-seq. Generates BAMs, bigWigs, peaks, nucleosome positions, and various QC metrics.
• wes: Whole genome/exome/targeted variant detection. Generates BAMs, VCFs, and various QC metrics.
• wgbs: WGBS methylation analysis.
• rrbs: RRBS methylation analysis.
• species: Species/metagenomics/contamination analysis.

Routes for comparing groups of samples

Some protocols require analysis of multiple samples simultaneously, such as tumor-normal or treatment-control combinations. There are additional routes for comparing groups of samples after individual samples are processed with a generic sample-centric route. These routes depend on the output of the generic routes and must be run from the same directory. Available comparison routes:

• rna-star-groups-dge: Differential gene expression for the rna-star results.
• wes-pairs-snv: Somatic variant detection for the wes or rna-snv results.
• chip-pairs-peaks: Peak calling for the chip results.

Each route has a description with more details regarding its output.