github.com/iwc-workflows/rnaseq-sr/main
Abstract
Complete RNA-Seq analysis for single-end data: Processes raw FASTQ data through adapter and bad quality removal (fastp), alignment with STAR using ENCODE parameters, gene quantification via multiple methods (STAR and featureCounts), and expression calculation (FPKM with Cufflinks/StringTie, normalized coverage with bedtools). Produces count tables, normalized expression values, and genomic coverage tracks. Supports stranded and unstranded libraries, generating both HTSeq-compatible counts and normalized measures for downstream analysis.
Fields of Study & Subjects
Genomics and Phylogenetic Studies
Single-cell and spatial transcriptomics
Gene expression and cancer classification
Publication details
- Journal / source
- Zenodo (CERN European Organization for Nuclear Research)
- Publication date
- 17 February 2026
- Language
- EN