From: QoRTs: a comprehensive toolset for quality control and data processing of RNA-Seq experiments
QoRTs | RSeQC | RNA-SeQC | |
---|---|---|---|
Sequence Metrics: | |||
Quality score (by cycle) | Yes | Yes1,* | Yes |
G/C content | Yes | Yes | Yes |
Nucleotide vs cycle (NVC) | Yes | Yes1 | No |
N-rate by cycle | Yes | No | No |
Unclipped NVC | Yes | No | No |
Clipped Sequences NVC | Yes | No | No |
Alignment Metrics: | |||
Strandedness | Yes | Yes2 | Yes |
Clipping Profile | Yes | Yes1,* | No |
Insert Size | Yes | Yes2,* | Partial3 |
Cigar Op Profile | Yes | Partial1,2,4,* | No |
Cigar Op Length Distribution | Yes | No | No |
Gene / Exon Coverage | |||
Gene-Body Coverage | Yes | Yes5,* | Yes |
Gene-Body Coverage, Low-/Medium-/High-expression genes | Yes | No | Yes |
Mapping Location rates (intron, exon, UTR, etc.) | Yes | Yes | Partial |
Gene Diversity | Yes | No | No |
RPKM/FPKM | Yes | Yes* | Yes |
“Wiggle” browser tracks | Yes | Yes5 | No |
Gene-level read counts for DESeq, edgeR | Yes | Partial | No |
Exon-level read counts for DEXSeq | Yes | No | No |
Splice Junction Metrics | |||
# Distinct Junction Loci, Known/Novel, High/Low coverage | Yes | Partial5 | No |
# Splice Junction Events, Known/Novel, High/Low coverage loci | Yes | Partial5 | No |
Splice junction coverage “.bed” browser tracks | Yes | No | No |
Coverage read-pair counts for all Junction Loci | Yes | No | No |
Visualization and Cross-Comparison | |||
Cross-Comparison between replicates | Yes | Partial6 | Partial6 |
Contrast by lane/run, biological group, etc. | Yes | No | No |
Generate Multiplots (png, svg, etc.) | Yes | No | No |
Generate QC reports (pdf) | Yes | No | No |