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Table 1 Features and capabilities of QoRTs compared with those offered by other tools

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

  1. RSeQC functions with documented flaws are marked with an asterisk (*); see the Additional file 2 for more information. (Note: 1Does not separately track read-pairs for paired-end data. 2Performs analysis on a subsample of input reads. 3Only calculates mean and standard deviation. 4Only profiles some cigar operations. 5No paired-end mode, may double-count overlapping paired reads. 6Generates comparison plots only for some metrics.)