rseqc-redux¶
Modernized RNA-seq Quality Control — a fork of RSeQC 5.0.1.
Quick start¶
What is rseqc-redux?¶
rseqc-redux provides 33 command-line tools for comprehensive quality control of RNA-seq data. It evaluates sequence quality, nucleotide composition, GC content, read distribution over genomic features, junction saturation, gene body coverage, and much more.
This is a modernized fork of RSeQC by Liguo Wang, with:
- Python 3.10+ support (tested on 3.10–3.13)
- 470+ automated tests
- Bug fixes and correctness improvements
- Modern packaging with
pyproject.toml
Tool categories¶
| Category | Tools |
|---|---|
| BAM Statistics | bam_stat, bam2fq, bam2wig, divide_bam, split_bam, split_paired_bam |
| Read Quality | read_quality, read_GC, read_NVC, read_hexamer, read_duplication, read_distribution |
| Alignment Profiles | clipping_profile, deletion_profile, insertion_profile, mismatch_profile |
| Gene Body & Expression | geneBody_coverage, geneBody_coverage2, FPKM_count, FPKM-UQ, RPKM_saturation, tin |
| Junction Analysis | junction_annotation, junction_saturation |
| Fragment & Strandedness | infer_experiment, inner_distance, RNA_fragment_size |
| BigWig Utilities | normalize_bigwig, overlay_bigwig |
| Single Cell | sc_bamStat, sc_editMatrix, sc_seqLogo, sc_seqQual |
Credits¶
Originally developed by Liguo Wang as RSeQC. Modernized and maintained by Nick Semenkovich.