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RNA-SeQC: RNA-seq metrics for quality control and process optimization

David S. DeLuca, Joshua Z. Levin, Andrey Sivachenko, Timothy Fennell, Marc-Danie Nazaire, Chris Williams, Michael Reich, Wendy Winckler, Gad Getz
2012 Computer applications in the biosciences : CABIOS  
In summary, RNA-SeQC provides quality control measures critical to experiment design, process optimization and downstream computational analysis.  ...  Availability and implementation: See www.genepattern.org to run online, or www.broadinstitute.org/rna-seqc/ for a command line tool.  ...  Here we present RNA-SeQC, a metrics tool with application to two domains: experiment design and process optimization; and quality control prior to computational analysis.  ... 
doi:10.1093/bioinformatics/bts196 pmid:22539670 pmcid:PMC3356847 fatcat:4ewifbak3vcqhkqvdvxhldht6y

Quality Control for RNA-Seq (QuaCRS): An Integrated Quality Control Pipeline

Karl W. Kroll, Nima E. Mokaram, Alexander R. Pelletier, David E. Frankhouser, Maximillian S. Westphal, Paige A. Stump, Cameron L. Stump, Ralf Bundschuh, James S. Blachly, Pearlly Yan
2014 Cancer Informatics  
QuaCRS (Quality Control for RNA-Seq) is an integrated, simplified quality control (QC) system for RNA-seq data that allows easy execution of several open-source QC tools, aggregation of their output, and  ...  First is the QC Pack wrapper, which executes three QC tools: FastQC, RNA-SeQC, and selected functions from RSeQC.  ...  David Lucas, Department of Internal Medicine, for his assistance in this manuscript. Author contributions  ... 
doi:10.4137/cin.s14022 pmid:25368506 pmcid:PMC4214596 fatcat:yedm4z42ebhw3paaqoxzko3riu

RNA-QC-chain: comprehensive and fast quality control for RNA-Seq data

Qian Zhou, Xiaoquan Su, Gongchao Jing, Songlin Chen, Kang Ning
2018 BMC Genomics  
Conclusions: We present here a tool, RNA-QC-Chain, which can be used to comprehensively resolve the quality control processes of RNA-Seq data effectively and efficiently.  ...  Results: We developed a comprehensive, fast and easy-to-use QC pipeline for RNA-Seq data, RNA-QC-Chain, which involves three steps: (1) sequencing-quality assessment and trimming; (2) internal (ribosomal  ...  Therefore, before downstream analysis, raw RNA-Seq data must be checked and processed by quality control (QC) procedures to ensure accurate transcript measurements and correct knowledge acquirements from  ... 
doi:10.1186/s12864-018-4503-6 pmid:29444661 pmcid:PMC5813327 fatcat:o3yatxqhszefraus3uc3an5hjy

mRIN for direct assessment of genome-wide and gene-specific mRNA integrity from large-scale RNA-sequencing data

Huijuan Feng, Xuegong Zhang, Chaolin Zhang
2015 Nature Communications  
control.  ...  Here we develop a method named mRIN to directly assess mRNA integrity from RNA-Seq data at the sample and individual gene level.  ...  Acknowledgements We thank Jonah Lee for proofreading of the manuscript.  ... 
doi:10.1038/ncomms8816 pmid:26234653 pmcid:PMC4523900 fatcat:efqbqitpy5dufhstmbntv6wrxa

Analysis of Whole Transcriptome Sequencing Data: Workflow and Software

In Seok Yang, Sangwoo Kim
2015 Genomics & Informatics  
RNA-seq is a powerful technique for characterizing and quantifying the transcriptome and accelerates the development of bioinformatics software.  ...  RNA is a polymeric molecule implicated in various biological processes, such as the coding, decoding, regulation, and expression of genes.  ...  Acknowledgments This work was supported by the Bio-Synergy Research Project (NRF-2014M3A9C4066449) of the Ministry of Science, ICT and Future Planning through the National Research Foundation.  ... 
doi:10.5808/gi.2015.13.4.119 pmid:26865842 pmcid:PMC4742321 fatcat:y4q3sgeckbbpdmcgnpmakhlvku

GenPipes: an open-source framework for distributed and scalable genomic analyses [article]

Mathieu Bourgey, Rola Dali, Robert Eveleigh, Kuang Chung Chen, Louis Letourneau, Joel Fillon, Marc Michaud, Maxime Caron, Johanna Sandoval, Francois Lefebvre, Gary Leveque, Eloi Mercier (+11 others)
2018 bioRxiv   pre-print
GenPipes already implements 12 validated and scalable pipelines for various genomics applications, including RNA-Seq, ChIP-Seq, DNA-Seq, Methyl-Seq, Hi-C, capture Hi-C, metagenomics and PacBio long read  ...  Here we present GenPipes, a flexible Python-based framework that facilitates the development and deployment of multi-step workflows optimized for High Performance Computing clusters and the cloud.  ...  Several common quality metrics (rRNA content, expression saturation estimation etc.) are also calculated through the use of RNA-SeQC [27] and inhouse scripts.  ... 
doi:10.1101/459552 fatcat:po4uhoz5ozezffdk7hejdl62ia

Comparing reference-based RNA-Seq mapping methods for non-human primate data

Ashlee M Benjamin, Marshall Nichols, Thomas W Burke, Geoffrey S Ginsburg, Joseph E Lucas
2014 BMC Genomics  
Due limited availability of genomic resources for under-characterized species, RNA-Seq is a popular method of choice for transcriptome analyses.  ...  We present a comparison of reference-based mapping methods for RNA-Seq data originating from Non-Human Primates (NHPs), and their implications in downstream differential expression analysis.  ...  We would also like to acknowledege BE, LH, CW, KW, BK, BN, CM, MB, and TV for helpful discussions.  ... 
doi:10.1186/1471-2164-15-570 pmid:25001289 pmcid:PMC4112205 fatcat:cu6e3zz7g5c4taih4bgkyocewe

GenPipes: an open-source framework for distributed and scalable genomic analyses

Mathieu Bourgey, Rola Dali, Robert Eveleigh, Kuang Chung Chen, Louis Letourneau, Joel Fillon, Marc Michaud, Maxime Caron, Johanna Sandoval, Francois Lefebvre, Gary Leveque, Eloi Mercier (+11 others)
2019 GigaScience  
With the decreasing cost of sequencing and the rapid developments in genomics technologies and protocols, the need for validated bioinformatics software that enables efficient large-scale data processing  ...  We would also like to acknowledge Romain Gregoire and Tushar Dubey for their contribution to the code and Patricia Goerner-Potvin for her help in planning the report content.  ...  Acknowledgements Data analyses were enabled by compute and storage resources provided by Compute Canada and Calcul Qu ébec.  ... 
doi:10.1093/gigascience/giz037 pmid:31185495 pmcid:PMC6559338 fatcat:rqn3brcaazajrhmm2boqynaaee

Sequencing of first-strand cDNA library reveals full-length transcriptomes

Saurabh Agarwal, Todd S. Macfarlan, Maureen A. Sartor, Shigeki Iwase
2015 Nature Communications  
However, many current methods for ssRNA-seq suffer from the underrepresentation of both the 5′ and 3′ ends of RNAs, which can be attributed to second-strand cDNA synthesis.  ...  Massively parallel strand-specific sequencing of RNA (ssRNA-seq) has emerged as a powerful tool for profiling complex transcriptomes.  ...  Mueller and John Kim in the Department of Human Genetics at the University of Michigan for their critical readings and suggestions for the manuscript.  ... 
doi:10.1038/ncomms7002 pmid:25607527 pmcid:PMC5054741 fatcat:sntrj563wfezdmwydsy7l44b2a

Analysis of the transcriptome in molecular epidemiology studies

Cliona M. McHale, Luoping Zhang, Reuben Thomas, Martyn T. Smith
2013 Environmental and Molecular Mutagenesis  
Analysis of datasets at the pathway level can compensate for some of the limitations of RNA-Seq and, as more datasets become available, will increasingly elucidate the exposure-disease continuum.  ...  The third phase of the MicroArray Quality Control Consortium project (MAQC-III), also called Sequencing Quality Control (SeQC), aims to address these limitations through standardization of experimental  ...  Acknowledgments Our studies on benzene described here were supported by National Institutes of Health grant (P42ES004705 to M.T.S) and by EPA contract number EP-11-001398.  ... 
doi:10.1002/em.21798 pmid:23907930 pmcid:PMC5142298 fatcat:scpf4xrgazbi7ps4b65kgy5vgy

RNA-sequencing in ophthalmology research: considerations for experimental design and analysis

Nicholas Owen, Mariya Moosajee
2019 Therapeutic Advances in Ophthalmology  
But with a wide range of applications, the design of such experiments can be problematic, no single optimal pipeline exists, and therefore, several considerations must be undertaken for optimal study design  ...  RNA-sequencing accurately snapshots thousands of genes, capturing many subtypes of RNA molecules, and has become the gold standard for transcriptome gene expression quantification.  ...  Conflict of interest statement The authors declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.  ... 
doi:10.1177/2515841419835460 pmid:30911735 pmcid:PMC6421592 fatcat:boslyh2lsvclthytlgouxa4emi

CLEAR: coverage-based limiting-cell experiment analysis for RNA-seq

Logan A. Walker, Michael G. Sovic, Chi-Ling Chiang, Eileen Hu, Jiyeon K. Denninger, Xi Chen, Elizabeth D. Kirby, John C. Byrd, Natarajan Muthusamy, Ralf Bundschuh, Pearlly Yan
2020 Journal of Translational Medicine  
CLEAR fills an important niche in pre-processing lcRNA-seq data to facilitate transcriptome profiling and DEG analysis.  ...  Direct cDNA preamplification protocols developed for single-cell RNA-seq have enabled transcriptome profiling of precious clinical samples and rare cell populations without the need for sample pooling  ...  Software availability and requirements Project Name: CLEAR. Project Home Page: https ://githu b.com/rbund schuh /CLEAR . Operating system(s): Linux. Programming Language: Python.  ... 
doi:10.1186/s12967-020-02247-6 pmid:32039730 fatcat:n2bvw75r7jfrtezuu2n7qttqqi

Effects of Different Sources of Fat in the Diet of Pigs on the Liver Transcriptome Estimated by RNA-Seq

Maria Oczkowicz, Małgorzata Świątkiewicz, Katarzyna Ropka-Molik, Artur Gurgul, Kacper Żukowski
2016 Annals of Animal Science  
Using the RNA-Seq method we identified 39 differentially expressed genes (DEGs) as a result of Cuffdiff analysis of the differences among all groups.  ...  in oxidoreductase and catalytic activity.  ...  RNA-SeQC: RNA-seq metrics for quality control and process optimization. Bioinformatics, 28: 1530-1532. D o d t M., R o e h r J.T., A h m e d R., D i e t e r i c h C. (2012).  ... 
doi:10.1515/aoas-2016-0033 fatcat:5kstxcwzfzfwhf5k3f273hh4ze

Comprehensive evaluation of RNA-seq analysis pipelines in diploid and polyploid species

Miriam Payá-Milans, James W Olmstead, Gerardo Nunez, Timothy A Rinehart, Margaret Staton
2018 GigaScience  
In addition, researchers are faced with many options for RNA-seq data processing and limited information on how their decisions will impact the final outcome.  ...  The selection of bioinformatic software tools for RNA-seq data analysis can maximize quality parameters on de novo assemblies and availability of reads in downstream analysis.  ...  Collante for their skillful support in RNA extraction and preparing libraries for sequencing, and Sun Xiaocun for support in statistics.  ... 
doi:10.1093/gigascience/giy132 pmid:30418578 pmcid:PMC6275443 fatcat:2bgfv3cdkfa4lb57i6kiu7qrp4

Identification of genes expressed in a mesenchymal subset regulating prostate organogenesis using tissue and single cell transcriptomics

Nadia Boufaied, Claire Nash, Annie Rochette, Anthony Smith, Brigid Orr, O. Cathal Grace, Yu Chang Wang, Dunarel Badescu, Jiannis Ragoussis, Axel A. Thomson
2017 Scientific Reports  
We would like to thank Nicola Regan for help with graphics, and the Genepool/ Edinburgh Genomics for Tag-seq library construction and sequencing.  ...  Additionally, Dr Nadia Boufaied was supported by Prostate Cancer Canada and the Movember Foundation -Grant #T2014-01.  ...  Various quality controls from the RNA-SeQC package were used 47 , including the genes detected, mapping rates, duplication rates, and intronic rate, based on metrics collected for each sample used.  ... 
doi:10.1038/s41598-017-16685-8 pmid:29180763 pmcid:PMC5703996 fatcat:zzgo47ugtfdvpeetiozxyp54f4
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