Details in the evaluation of circular RNA detection tools: Reply to Chen and Chuang

In their comment, Chen and Chuang [1] pointed out several weak points of our recent paper [2]. Here we respond in detail to clarify the dataset we used in our work. We also discuss the three confounding factors they listed in their comment.

[1]  Derek Y. Chiang,et al.  MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery , 2010, Nucleic acids research.

[2]  Tim Schneider,et al.  Exon circularization requires canonical splice signals. , 2015, Cell reports.

[3]  Sebastian D. Mackowiak,et al.  Circular RNAs are a large class of animal RNAs with regulatory potency , 2013, Nature.

[4]  Petar Glažar,et al.  circBase: a database for circular RNAs , 2014, RNA.

[5]  F. Zhao,et al.  CIRI: an efficient and unbiased algorithm for de novo circular RNA identification , 2015, Genome Biology.

[6]  Jun Zhang,et al.  Diverse alternative back-splicing and alternative splicing landscape of circular RNAs , 2016, Genome research.

[7]  Linda Szabo,et al.  Statistically based splicing detection reveals neural enrichment and tissue-specific induction of circular RNA during human fetal development , 2015, Genome Biology.

[8]  Trees-Juen Chuang,et al.  Comment on "A comprehensive overview and evaluation of circular RNA detection tools" , 2019, PLoS Comput. Biol..

[9]  J. Salzman,et al.  Detecting circular RNAs: bioinformatic and experimental challenges , 2016, Nature Reviews Genetics.

[10]  David Haussler,et al.  The UCSC Known Genes , 2006, Bioinform..

[11]  Kai Wang,et al.  Circular RNA profile in gliomas revealed by identification tool UROBORUS , 2016, Nucleic acids research.

[12]  Julia Salzman,et al.  Cell-Type Specific Features of Circular RNA Expression , 2013, PLoS genetics.

[13]  Wei Lin,et al.  A comprehensive overview and evaluation of circular RNA detection tools , 2017, PLoS Comput. Biol..

[14]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[15]  J. Kjems,et al.  Natural RNA circles function as efficient microRNA sponges , 2013, Nature.