rpd-rnaseq is a bioinformatics best-practice analysis pipeline for bulk RNAseq analyis and was developed by the Research Pipeline Development Team at the Genome Institute of Singapore (GIS) based on a request by the Cancer Therapeutics & Stratified Oncology 6.
The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It further comes with Conda, Docker and Singularity support, making software installation easy and results reproducible.
The pipeline itself is mostly based on the GIS STAR-RSEM pipeline (2017-10) and nf-core/rnaseq. The implementation tries to stay in line with nf-core practices and recommendations.
| Step | Main program/s |
|---|---|
| Trimmming, combining of read-pairs per sample and QC | Trim Galore, FastQC |
| Mapping | STAR |
| Visualization files (bigWigs) | Samtools, deepTools (bamCoverage) |
| RNASeq Metrics | CollectRnaSeqMetrics (Picard) |
| RNASeq QC | RSeQC |
| Gene and isoform expression | RSEM |
| QC report | MultiQC |
Documentation about the pipeline can be found in the docs/ directory: