TY - JOUR
T1 - MiRSeq
T2 - A user-friendly standalone toolkit for sequencing quality evaluation and miRNA profiling
AU - Pan, Cheng Tsung
AU - Tsai, Kuo Wang
AU - Hung, Tzu Min
AU - Lin, Wei Chen
AU - Pan, Chao Yu
AU - Yu, Hong Ren
AU - Li, Sung Chou
N1 - Publisher Copyright:
© 2014 Cheng-Tsung Pan et al.
PY - 2014
Y1 - 2014
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=84927794928&partnerID=8YFLogxK
U2 - 10.1155/2014/462135
DO - 10.1155/2014/462135
M3 - 文章
C2 - 25114903
AN - SCOPUS:84927794928
SN - 2314-6133
VL - 2014
JO - BioMed Research International
JF - BioMed Research International
M1 - 462135
ER -