1 Overview¶
RiboParser is designed for complete RNA-seq and ribosome profiling data analysis. This page only provides the conceptual overview; detailed commands are placed in the workflow pages to avoid duplication.
What RiboParser does¶
The complete workflow consists of two parts: a public pipeline that can be handled by general bioinformatics tools, and the RiboParser-specific analysis described below.
Public pipeline (general tools):
- reference preparation for transcriptome-aware Ribo-seq analysis
- RNA-seq and Ribo-seq raw data cleaning
- contaminant classification against rRNA, tRNA, ncRNA, mRNA, and genome indexes
- splice-aware genome alignment
- transcriptome quantification
RiboParser-specific analysis:
- Ribo-seq quality control
- P-site offset inference
- RNA/Ribo read density construction
- merged density matrix generation
- periodicity, metaplot, coverage, and correlation analysis
- gene-level quantification and read-density retrieval
- codon-level pausing, occupancy, decoding time, selection time, variation, and odds-ratio analysis
- smORF scanning, clustering, Ribo-seq evidence evaluation, and quantification
- SeRP signal and peak analysis
- helper utilities for FASTA, FASTQ, bedGraph, Bowtie logs, RSEM tables, and merged Ribo-seq outputs