Tool Overview¶
rseqc-redux provides 33 command-line tools for RNA-seq quality control. All tools follow the same pattern:
All tools¶
BAM Statistics¶
| Tool | Description |
|---|---|
| bam_stat.py | Summarize mapping statistics of a BAM file |
| bam2fq.py | Convert BAM alignments to FASTQ format |
| bam2wig.py | Convert BAM file to wiggle format |
| divide_bam.py | Equally divide BAM file into n parts |
| split_bam.py | Split BAM by gene list |
| split_paired_bam.py | Split paired-end BAM into two single-end BAMs |
Read Quality¶
| Tool | Description |
|---|---|
| read_quality.py | Phred quality score distribution across read positions |
| read_GC.py | GC content distribution of reads |
| read_NVC.py | Nucleotide frequency per read position (NVC plot) |
| read_hexamer.py | Hexamer frequency analysis |
| read_duplication.py | Sequence- and mapping-based duplication rates |
| read_distribution.py | Read distribution over genomic features |
Alignment Profiles¶
| Tool | Description |
|---|---|
| clipping_profile.py | Soft-clipping profile across read positions |
| deletion_profile.py | Deletion distribution across read positions |
| insertion_profile.py | Insertion distribution across read positions |
| mismatch_profile.py | Mismatch distribution across read positions |
Gene Body & Expression¶
| Tool | Description |
|---|---|
| geneBody_coverage.py | RNA-seq read coverage over gene body |
| geneBody_coverage2.py | Gene body coverage from BigWig input |
| FPKM_count.py | Raw count, FPM, and FPKM per gene |
| FPKM-UQ.py | Count, FPKM, and FPKM-UQ per gene |
| RPKM_saturation.py | RPKM saturation analysis |
| tin.py | Transcript integrity number |
Junction Analysis¶
| Tool | Description |
|---|---|
| junction_annotation.py | Annotate splice junctions against gene model |
| junction_saturation.py | Junction discovery saturation analysis |
Fragment & Strandedness¶
| Tool | Description |
|---|---|
| infer_experiment.py | Infer strandedness of RNA-seq experiment |
| inner_distance.py | Inner distance (insert size) of RNA-seq fragments |
| RNA_fragment_size.py | Fragment size statistics per gene |
BigWig Utilities¶
| Tool | Description |
|---|---|
| normalize_bigwig.py | Normalize BigWig signal to fixed wigsum |
| overlay_bigwig.py | Pairwise operations on two BigWig files |
Single Cell¶
| Tool | Description |
|---|---|
| sc_bamStat.py | Single-cell RNA-seq mapping statistics |
| sc_editMatrix.py | Barcode/UMI error correction heatmaps |
| sc_seqLogo.py | DNA sequence logo from FASTQ/FASTA |
| sc_seqQual.py | Sequencing quality heatmap from FASTQ |