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references.bib

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+@article{hsieh2019effect,
+  title={Effect of de novo transcriptome assembly on transcript quantification},
+  author={Hsieh, Ping-Han and Oyang, Yen-Jen and Chen, Chien-Yu},
+  journal={Scientific reports},
+  volume={9},
+  number={1},
+  pages={8304},
+  year={2019},
+  publisher={Nature Publishing Group UK London},
+  url={https://www.nature.com/articles/s41598-019-44499-3}
+}
+
+@article{wang2017comprehensive,
+  title={Comprehensive evaluation of de novo transcriptome assembly programs and their effects on differential gene expression analysis},
+  author={Wang, Sufang and Gribskov, Michael},
+  journal={Bioinformatics},
+  volume={33},
+  number={3},
+  pages={327--333},
+  year={2017},
+  publisher={Oxford University Press},
+  url={https://academic.oup.com/bioinformatics/article/33/3/327/2580374}
+}
+
+@article{marioni2008rna,
+  title={RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays},
+  author={Marioni, John C and Mason, Christopher E and Mane, Shrikant M and Stephens, Matthew and Gilad, Yoav},
+  journal={Genome research},
+  volume={18},
+  number={9},
+  pages={1509--1517},
+  year={2008},
+  publisher={Cold Spring Harbor Lab},
+  url={https://genome.cshlp.org/content/18/9/1509.long}
+}
+
+@article{conesa2016survey,
+  title={A survey of best practices for RNA-seq data analysis},
+  author={Conesa, Ana and Madrigal, Pedro and Tarazona, Sonia and Gomez-Cabrero, David and Cervera, Alejandra and McPherson, Andrew and Szcze{\'s}niak, Micha{\l} Wojciech and Gaffney, Daniel J and Elo, Laura L and Zhang, Xuegong and others},
+  journal={Genome biology},
+  volume={17},
+  number={1},
+  pages={1--19},
+  year={2016},
+  publisher={BioMed Central}
+}
+
+@article{schurch2016many,
+  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},
+  journal={Rna},
+  volume={22},
+  number={6},
+  pages={839--851},
+  year={2016},
+  publisher={Cold Spring Harbor Lab},
+  url={https://rnajournal.cshlp.org/content/early/2016/03/30/rna.053959.115.abstract}
+}
+
+@article{hart2013calculating,
+  title={Calculating sample size estimates for RNA sequencing data},
+  author={Hart, Steven N and Therneau, Terry M and Zhang, Yuji and Poland, Gregory A and Kocher, Jean-Pierre},
+  journal={Journal of computational biology},
+  volume={20},
+  number={12},
+  pages={970--978},
+  year={2013},
+  publisher={Mary Ann Liebert, Inc. 140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 USA},
+  url={https://www.liebertpub.com/doi/10.1089/cmb.2012.0283}
+}
+
+@article{zhao2018rnaseqsamplesize,
+  title={RnaSeqSampleSize: real data based sample size estimation for RNA sequencing},
+  author={Zhao, Shilin and Li, Chung-I and Guo, Yan and Sheng, Quanhu and Shyr, Yu},
+  journal={BMC bioinformatics},
+  volume={19},
+  number={1},
+  pages={1--8},
+  year={2018},
+  publisher={BioMed Central},
+  url={https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2191-5}
+}
+
+@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},
+  volume={12},
+  number={1},
+  pages={1--13},
+  year={2014},
+  publisher={BioMed Central},
+  url={https://bmcbiol.biomedcentral.com/articles/10.1186/1741-7007-12-42}
+}
+
+@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},
+  volume={16},
+  number={1},
+  pages={1--14},
+  year={2015},
+  publisher={BioMed Central},
+  url={https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4559181/}
+}
+
+@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},
+  journal={Nature methods},
+  volume={7},
+  number={9},
+  pages={709--715},
+  year={2010},
+  publisher={Nature Publishing Group US New York},
+  url={https://www.nature.com/articles/nmeth.1491}
+}
+
+@article{daley2013predicting,
+  title={Predicting the molecular complexity of sequencing libraries},
+  author={Daley, Timothy and Smith, Andrew D},
+  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}
+}
+
+@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},
+  url={https://www.nature.com/articles/nmeth.4106}
+}
+
+@article{sigurgeirsson2014sequencing,
+  title={Sequencing degraded RNA addressed by 3'tag counting},
+  author={Sigurgeirsson, Benjamin and Emanuelsson, Olof and Lundeberg, Joakim},
+  journal={PloS one},
+  volume={9},
+  number={3},
+  pages={e91851},
+  year={2014},
+  publisher={Public Library of Science San Francisco, USA},
+  url={https://pubmed.ncbi.nlm.nih.gov/24632678/}
+}
+
+@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},
+  journal={BMC genomics},
+  volume={14},
+  number={1},
+  pages={1--12},
+  year={2013},
+  publisher={BioMed Central},
+  url={https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-167}
+}
+
+@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},
+  pages={e3091},
+  year={2017},
+  publisher={PeerJ Inc.},
+  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},
+  volume={6},
+  number={1},
+  pages={25533},
+  year={2016},
+  publisher={Nature Publishing Group UK London},
+  url={https://www.nature.com/articles/srep25533}
+}
+
+@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},
+  journal={Genome biology},
+  volume={12},
+  number={3},
+  pages={1--14},
+  year={2011},
+  publisher={BioMed Central}
+}
+
+@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},
+  year={2015},
+  publisher={Faculty of 1000 Ltd}
+}
+
+@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},
+  pages={1--11},
+  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},
+  pages={1--12},
+  year={2016},
+  publisher={BioMed Central}
+}
+
+@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},
+  journal={Bioinformatics},
+  volume={32},
+  number={24},
+  pages={3836--3838},
+  year={2016},
+  publisher={Oxford University Press}
+}
+
+@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},
+  year={2015},
+  publisher={Oxford University Press}
+}
+
+@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},
+  journal={Theory in biosciences},
+  volume={131},
+  pages={281--285},
+  year={2012},
+  publisher={Springer}
+}