title: miRSeq: a user-friendly standalone toolkit for sequencing quality evaluation and miRNA profiling.
abstract: MicroRNAs (miRNAs) present diverse regulatory functions in a wide range of biological activities. Studies on miRNA functions generally depend on determining miRNA expression profiles between libraries by using a next-generation sequencing (NGS) platform. Currently, several online web services are developed to provide small RNA NGS data analysis. However, the submission of large amounts of NGS data, conversion of data format, and limited availability of species bring problems. In this study, we developed miRSeq to provide alternatives. To test the performance, we had small RNA NGS data from four species, including human, rat, fly, and nematode, analyzed with miRSeq. The alignments results indicate that miRSeq can precisely evaluate the sequencing quality of samples regarding percentage of self-ligation read, read length distribution, and read category. miRSeq is a user-friendly standalone toolkit featuring a graphical user interface (GUI). After a simple installation, users can easily operate miRSeq on a PC or laptop by using a mouse. Within minutes, miRSeq yields useful miRNA data, including miRNA expression profiles, 3' end modification patterns, and isomiR forms. Moreover, miRSeq supports the analysis of up to 105 animal species, providing higher flexibility.
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan.
authors.forename: Cheng-Tsung
authors.initials: CT
authors.lastname: Pan
authors.affiliation: Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.
authors.forename: Kuo-Wang
authors.initials: KW
authors.lastname: Tsai
authors.affiliation: Genomics & Proteomics Core Laboratory, Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.
authors.forename: Tzu-Min
authors.identifier: 0000-0003-2275-5247
authors.initials: TM
authors.lastname: Hung
authors.affiliation: Department of Parasitology, National Cheng Kung University College of Medicine, Tainan, Taiwan.
authors.forename: Wei-Chen
authors.identifier: 0000-0001-7223-5931
authors.initials: WC
authors.lastname: Lin
authors.affiliation: Genomics & Proteomics Core Laboratory, Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.
authors.forename: Chao-Yu
authors.identifier: 0000-0001-9066-6583
authors.initials: CY
authors.lastname: Pan
authors.affiliation: Departments of Pediatrics, Chang Gung Memorial Hospital-Kaohsiung Medical Center, Graduate Institute of Clinical Medical Science, Chang Gung University College of Medicine, Kaohsiung, Taiwan.
authors.forename: Hong-Ren
authors.identifier: 0000-0003-1242-8760
authors.initials: HR
authors.lastname: Yu
authors.affiliation: Genomics & Proteomics Core Laboratory, Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan ; Children's Hospital, 12th Floor, No. 123, Dapi Road, Niaosong District, Kaohsiung 83301, Taiwan.
authors.forename: Sung-Chou
authors.identifier: 0000-0002-3016-9718
authors.initials: SC
authors.lastname: Li
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans; D002460:Cell Line; D019295:Computational Biology / Q000379:methods; D004331:Drosophila melanogaster; D020869:Gene Expression Profiling / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D059467:Transcriptome / Q000235:genetics*
chemical_list: D035683:MicroRNAs