RSeQC protocols

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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

 (54)
2018
PMCID: 5780744
PMID: 29363429
DOI: 10.1186/s12864-017-4339-5

[…] two replicates were present for monocytes cd14+ cells, cd20+ b cells, h1-hesc, ipsc, huvec, imr90, mcf-7, and hmec and a single one for cd4+ t cells. rpkms of the rna-seq data were calculated using rseqc []. for monocytes, blueprint rna-seq rpkm data (gse58310, gse58310_geneexpression.csv.gz, monocytes_day0_rpmi) was also used []. based on rpkm, ucsc transcripts with expression levels among top […]

2018
PMCID: 5829742
PMID: 29309643
DOI: 10.1093/nar/gkx1306

[…] the rna-seq libraries were sequenced as 51 nt pair-end reads at one sample per lane of an illumina hiseq 2500, generating an average of 265 million reads per sample. fragment size was estimated by rseqc using the first 1 000 000 read pairs that were uniquely mapped (). all reads were aligned to the human reference genome (hg19/grch37) by tophat 2.0.9 using these options: […]

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 ). the saturation of lncrna from rna-seq was measured by rseqc and the result is shown in figure , and the cluster or pca results were shown in figure . these results indicate that the quality of rna-seq is good and reliable., cpc was used to predict […]

2018
PMCID: 5867869
PMID: 29518982
DOI: 10.3390/genes9030148

[…] were obtained from the ncbi genome database (https://www.ncbi.nlm.nih.gov/genome/). a summary of mapping statistics was obtained using bam_stat.py implemented in the rna sequencing quality control (rseqc) package []. mapped reads were filtered based on mapping quality and only uniquely mapped reads (mapping quality > 10) were used for further analysis. high-throughput sequencing […]


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RSeQC in publications

 (153)
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 […]

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 […]

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 […]

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 […]

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 […]


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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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