RSeQC pipeline

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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Publications for RSeQC

RSeQC IN pipelines

 (23)
2018
PMCID: 5845709
PMID: 29559983
DOI: 10.3389/fpls.2018.00244

[…] and the results indicated that the average alignment coverage was nearly 58% in all samples; uniquely mapped genes were about 46% (table s1). the saturation of lncrna from rna-seq was measured by rseqc and the result is shown in figure s1, and the cluster or pca results were shown in figure s2. these results indicate that the quality of rna-seq is good and reliable., cpc was used to predict […]

2018
PMCID: 5902896
PMID: 29661164
DOI: 10.1186/s12885-018-4215-y

[…] as well as predict and estimate expression of novel isoforms. pre- and post-alignment quality control was performed with fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and rseqc (http://rseqc.sourceforge.net/), respectively., a total of 171 patients with resected stage i-ii nsclc collected at university health network (toronto, canada) were included in this study. […]

2017
PMCID: 5253647
PMID: 28102363
DOI: 10.1038/ncomms14098

[…] check the sequencing quality, and high-quality reads were mapped to human reference genome (hg19) along with the gene annotation data (genecode v19) from the genecode database using star (v2.4.2)61. rseqc was applied for assessing rna sample quality62. gene-level expression was reported in fragments per kilobase per million reads by cufflinks63. raw rna-seq data will be deposited to sra database […]

2017
PMCID: 5369198
PMID: 28347287
DOI: 10.1186/s12870-017-1008-4

[…] 100-bp paired-end reads. sequencing reads were analyzed with casava software (illumina inc., san diego, ca, usa) for demultiplexing and fastq file generation. the quality of reads was checked using rseqc software [25]., rnaseq reads were aligned on s. lycopersicum cv. heinz 1706 version 2.40 genome, san marzano and vesuviano [20] respective genome using tophat (ver. 2.0.6). transcriptome […]

2017
PMCID: 5374493
PMID: 28361917
DOI: 10.1038/srep45073

[…] nidulans genome assembly version s10-m03-r07 (release on 02-mar-2014, available in the aspgd). saturation of known splice junctions was verified using the junction_saturation function from the rseqc package62, in order to check for proper sequencing depth. transcriptome analysis was carried out using cufflinks v.2.1 as follows: transcript assembly and quantification for each library […]

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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