RSeQC specifications

Information


Unique identifier OMICS_01235
Name RSeQC
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format SAM, BAM, BED
Operating system Unix/Linux
Programming languages C, Python
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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RSeQC articles

RSeQC citations

 (6)
2018
PMCID: 5770019

[…] number of aligned reads, total number of uniquely aligned reads, genes and transcripts detected, ribosomal fraction known junction saturation, and read distribution over known gene models using rseqc version 2.3 [26]. all gene-level and transcript counts were then imported into the r bioconductor edger package [27, 28]. the trended mean of m values (tmm) were normalized to account […]

2017
PMCID: 5779945

[…] significant difference., the overall raw reads of the eight samples fell in the range of 46,000,000–82,000,000. through strict quality checks, >95% of the reads had a quality score of ≥q20. the rseqc package was used to analyze the sequencing quality (27). the raw sequence data of each sample produced ~6 gb of data. of the total raw reads, 96.5% (~5.87±2.15×107 reads) were mapped onto […]

2017
PMCID: 5516136

[…] read summarization program from the subread package (v1.4.6) (liao, smyth, & shi, 2014). to study the distribution of the reads across features, the read_distribution function of the rseqc (v2.6.4) package (wang, wang, & li, 2012) was used. differentially expressed genes were identified using deseq2 v1.14.1 with default parameters. for go analysis, the orthologs of p. vivax […]

2016
PMCID: 4798287

[…] of the low quality bases (quality value ≤ 5) is greater than 50%. statistics analysis and evaluation of data were performed, including total raw reads, total clean reads, q20, q30 and gc content. rseqc software was used to quality-evaluate of all the data of rna-seq [27]. all downstream analyses were based on the quality-control clean reads. to evaluate the variation in gene expression, clean […]

2015
PMCID: 4640133

[…] any 5′ to 3′ bias in the data, a gene body coverage analysis was conducted. the gene body coverage of the mapped reads for all libraries were determined using the genebodycoverage.py script from the rseqc package and showed no significant 5′ or 3′ end bias (supplementary figs s3, s4 and supplementary file 4). to check for sample swaps a xistvschry analysis as published by ‘t hoen et al. 13 was […]

RSeQC institution(s)
Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA; State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China

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