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references.bib
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title={How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?},
author={Schurch, Nicholas J and Schofield, Piet{\'a} and Gierli{\'n}ski, Marek and Cole, Christian and Sherstnev, Alexander and Singh, Vijender and Wrobel, Nicola and Gharbi, Karim and Simpson, Gordon G and Owen-Hughes, Tom and others},
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@article{zhao2018rnaseqsamplesize,
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@article{gallego2014rna,
title={RNA-seq: impact of RNA degradation on transcript quantification},
author={Gallego Romero, Irene and Pai, Athma A and Tung, Jenny and Gilad, Yoav},
journal={BMC biology},
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@article{zhao2015comparison,
title={Comparison of stranded and non-stranded RNA-seq transcriptome profiling and investigation of gene overlap},
author={Zhao, Shanrong and Zhang, Ying and Gordon, William and Quan, Jie and Xi, Hualin and Du, Sarah and von Schack, David and Zhang, Baohong},
journal={BMC genomics},
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@article{levin2010comprehensive,
title={Comprehensive comparative analysis of strand-specific RNA sequencing methods},
author={Levin, Joshua Z and Yassour, Moran and Adiconis, Xian and Nusbaum, Chad and Thompson, Dawn Anne and Friedman, Nir and Gnirke, Andreas and Regev, Aviv},
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@article{daley2013predicting,
title={Predicting the molecular complexity of sequencing libraries},
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journal={Nature methods},
volume={10},
number={4},
pages={325--327},
year={2013},
publisher={Nature Publishing Group US New York},
url={https://www.nature.com/articles/nmeth.2375}
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@article{chhangawala2015impact,
title={The impact of read length on quantification of differentially expressed genes and splice junction detection},
author={Chhangawala, Sagar and Rudy, Gabe and Mason, Christopher E and Rosenfeld, Jeffrey A},
journal={Genome biology},
volume={16},
number={1},
pages={1--10},
year={2015},
publisher={BioMed Central},
url={https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4531809/}
}
@article{liu2014rna,
title={RNA-seq differential expression studies: more sequence or more replication?},
author={Liu, Yuwen and Zhou, Jie and White, Kevin P},
journal={Bioinformatics},
volume={30},
number={3},
pages={301--304},
year={2014},
publisher={Oxford University Press},
url={https://academic.oup.com/bioinformatics/article/30/3/301/228651}
}
@article{corley2017differentially,
title={Differentially expressed genes from RNA-Seq and functional enrichment results are affected by the choice of single-end versus paired-end reads and stranded versus non-stranded protocols},
author={Corley, Susan M and MacKenzie, Karen L and Beverdam, Annemiek and Roddam, Louise F and Wilkins, Marc R},
journal={BMC genomics},
volume={18},
number={1},
pages={1--13},
year={2017},
publisher={BioMed Central},
url={https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5442695/}
}
@article{liao2020read,
title={Read trimming is not required for mapping and quantification of RNA-seq reads at the gene level},
author={Liao, Yang and Shi, Wei},
journal={NAR genomics and bioinformatics},
volume={2},
number={3},
pages={lqaa068},
year={2020},
publisher={Oxford University Press},
url={https://pubmed.ncbi.nlm.nih.gov/33575617/}
}
@article{baruzzo2017simulation,
title={Simulation-based comprehensive benchmarking of RNA-seq aligners},
author={Baruzzo, Giacomo and Hayer, Katharina E and Kim, Eun Ji and Di Camillo, Barbara and FitzGerald, Garret A and Grant, Gregory R},
journal={Nature methods},
volume={14},
number={2},
pages={135--139},
year={2017},
publisher={Nature Publishing Group US New York},
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}
@article{sigurgeirsson2014sequencing,
title={Sequencing degraded RNA addressed by 3'tag counting},
author={Sigurgeirsson, Benjamin and Emanuelsson, Olof and Lundeberg, Joakim},
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year={2014},
publisher={Public Library of Science San Francisco, USA},
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@article{francis2013comparison,
title={A comparison across non-model animals suggests an optimal sequencing depth for de novotranscriptome assembly},
author={Francis, Warren R and Christianson, Lynne M and Kiko, Rainer and Powers, Meghan L and Shaner, Nathan C and D Haddock, Steven H},
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@article{klepikova2017effect,
title={Effect of method of deduplication on estimation of differential gene expression using RNA-seq},
author={Klepikova, Anna V and Kasianov, Artem S and Chesnokov, Mikhail S and Lazarevich, Natalia L and Penin, Aleksey A and Logacheva, Maria},
journal={PeerJ},
volume={5},
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url={https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5357343/}
}
@article{parekh2016impact,
title={The impact of amplification on differential expression analyses by RNA-seq},
author={Parekh, Swati and Ziegenhain, Christoph and Vieth, Beate and Enard, Wolfgang and Hellmann, Ines},
journal={Scientific reports},
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number={1},
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year={2016},
publisher={Nature Publishing Group UK London},
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@article{fu2018elimination,
title={Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers},
author={Fu, Yu and Wu, Pei-Hsuan and Beane, Timothy and Zamore, Phillip D and Weng, Zhiping},
journal={Bmc Genomics},
volume={19},
pages={1--14},
year={2018},
publisher={Springer}
}
@article{roberts2011improving,
title={Improving RNA-Seq expression estimates by correcting for fragment bias},
author={Roberts, Adam and Trapnell, Cole and Donaghey, Julie and Rinn, John L and Pachter, Lior},
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@article{soneson2015differential,
title={Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences},
author={Soneson, Charlotte and Love, Michael I and Robinson, Mark D},
journal={F1000Research},
volume={4},
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}
@article{zhang2017evaluation,
title={Evaluation and comparison of computational tools for RNA-seq isoform quantification},
author={Zhang, Chi and Zhang, Baohong and Lin, Lih-Ling and Zhao, Shanrong},
journal={BMC genomics},
volume={18},
number={1},
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year={2017},
publisher={BioMed Central}
}
@article{teng2016benchmark,
title={A benchmark for RNA-seq quantification pipelines},
author={Teng, Mingxiang and Love, Michael I and Davis, Carrie A and Djebali, Sarah and Dobin, Alexander and Graveley, Brenton R and Li, Sheng and Mason, Christopher E and Olson, Sara and Pervouchine, Dmitri and others},
journal={Genome biology},
volume={17},
number={1},
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@article{zindler2020simulating,
title={Simulating ComBat: how batch correction can lead to the systematic introduction of false positive results in DNA methylation microarray studies},
author={Zindler, Tristan and Frieling, Helge and Neyazi, Alexandra and Bleich, Stefan and Friedel, Eva},
journal={BMC bioinformatics},
volume={21},
pages={1--15},
year={2020},
publisher={Springer}
}
@article{manimaran2016batchqc,
title={BatchQC: interactive software for evaluating sample and batch effects in genomic data},
author={Manimaran, Solaiappan and Selby, Heather Marie and Okrah, Kwame and Ruberman, Claire and Leek, Jeffrey T and Quackenbush, John and Haibe-Kains, Benjamin and Bravo, Hector Corrada and Johnson, W Evan},
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volume={32},
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pages={3836--3838},
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@article{seyednasrollah2015comparison,
title={Comparison of software packages for detecting differential expression in RNA-seq studies},
author={Seyednasrollah, Fatemeh and Laiho, Asta and Elo, Laura L},
journal={Briefings in bioinformatics},
volume={16},
number={1},
pages={59--70},
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@article{dillies2013comprehensive,
title={A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis},
author={Dillies, Marie-Agn{\`e}s and Rau, Andrea and Aubert, Julie and Hennequet-Antier, Christelle and Jeanmougin, Marine and Servant, Nicolas and Keime, C{\'e}line and Marot, Guillemette and Castel, David and Estelle, Jordi and others},
journal={Briefings in bioinformatics},
volume={14},
number={6},
pages={671--683},
year={2013},
publisher={Oxford University Press}
}
@article{evans2018selecting,
title={Selecting between-sample RNA-Seq normalization methods from the perspective of their assumptions},
author={Evans, Ciaran and Hardin, Johanna and Stoebel, Daniel M},
journal={Briefings in bioinformatics},
volume={19},
number={5},
pages={776--792},
year={2018},
publisher={Oxford University Press}
}
@article{wagner2012measurement,
title={Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples},
author={Wagner, G{\"u}nter P and Kin, Koryu and Lynch, Vincent J},
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publisher={Springer}
}