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Protocols

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 citations

 (179)
library_books

A direct link between MITF, innate immunity, and hair graying

2018
PLoS Biol
PMCID: 5933715
PMID: 29723194
DOI: 10.1371/journal.pbio.2003648

[…] (v. 2.3.0e) software using default parameters. rna-seq reads that mapped to genomic locations for known rrnas (obtained from the ucsc genome browser) were filtered using split_bam.py included in the rseqc package (v. 2.3.7). rna-seq read counts were calculated with the htseq_count (v. 0.5.3p3) software using annotations for protein coding genes obtained from ensembl (release 67), thus obtaining […]

library_books

Global H3.3 dynamic deposition defines its bimodal role in cell fate transition

2018
Nat Commun
PMCID: 5906632
PMID: 29670118
DOI: 10.1038/s41467-018-03904-7

[…] illumina). library quality was analyzed on a bioanalyzer. high-throughput sequencing was performed on the hiseq 2500 (illumina)., quality control of the rna-seq raw files was performed using rseqc software and seqmonk (https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/). this was followed by mapping to mm9 genome assembly using star aligner. reads with more than two mismatches […]

library_books

Unifying cancer and normal RNA sequencing data from different sources

2018
Sci Data
PMCID: 5903355
PMID: 29664468
DOI: 10.1038/sdata.2018.61

[…] project for long rna-seq pipeline. samples with alignment rates less than 40% were excluded from further analysis., the software tools fastqc, picard (http://picard.sourceforge.net/index.shtml), rseqc, and mrin were used to evaluate sample quality. rna degradation, as detected by mrna, was present in some gtex and tcga samples. since degradation can bias expression level measurements […]

call_split

Helicase like transcription factor expression is associated with a poor prognosis in Non Small Cell Lung Cancer (NSCLC)

2018
BMC Cancer
PMCID: 5902896
PMID: 29661164
DOI: 10.1186/s12885-018-4215-y
call_split See protocol

[…] 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. […]

library_books

Adar3 Is Involved in Learning and Memory in Mice

2018
Front Neurosci
PMCID: 5914295
PMID: 29719497
DOI: 10.3389/fnins.2018.00243

[…] against assembly grcm38.p4 of the mouse genome with star v2.5.1a (dobin et al., ) using a pre-built index based on gencode m10. statistics and quality control of the alignment was performed with rseqc v2.6.1 (wang et al., ). quantification of the aligned reads was performed with rsem v1.2.26 (li and dewey, ). genes with low counts were filtered out and only genes with 10 counts in at least 2 […]

library_books

Dynamic transcriptome landscape of Asian domestic honeybee (Apis cerana) embryonic development revealed by high quality RNA sequencing

2018
BMC Dev Biol
PMCID: 5899340
PMID: 29653508
DOI: 10.1186/s12861-018-0169-1

[…] to index the genomes. the mapping statistics and the coverage of the gene body by the rna-seq reads were calculated by using bam_stat.py and genebody_coverage2.py, respectively, implemented in the rseqc package []., we applied a reference-based transcript assembler, stringtie [], to assemble the transcripts for each tested embryo sample. the gffcompare program […]


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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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