Benchmarking sequencing methods and tools that facilitate the study of alternative polyadenylation

被引:0
|
作者
Ankeeta Shah
Briana E. Mittleman
Yoav Gilad
Yang I. Li
机构
[1] University of Chicago,Genetics, Genomics, and Systems Biology
[2] University of Chicago,Section of Genetic Medicine, Department of Medicine
[3] University of Chicago,Department of Human Genetics
来源
关键词
Benchmarking; Alternative polyadenylation; RNA processing; Isoform analysis; RNA-seq; 3′-Seq; PacBio Iso-Seq; Long-read sequencing; QTL;
D O I
暂无
中图分类号
学科分类号
摘要
引用
收藏
相关论文
共 50 条
  • [31] IVT-SAPAS: Low-Input and Rapid Method for Sequencing Alternative Polyadenylation Sites
    Fu, Yonggui
    Ge, Yutong
    Sun, Yu
    Liang, Jiahui
    Wan, Liang
    Wu, Xiaojian
    Xu, Anlong
    PLOS ONE, 2015, 10 (12):
  • [32] Transcriptome dynamics through alternative polyadenylation in developmental and environmental responses in plants revealed by deep sequencing
    Shen, Yingjia
    Venu, R. C.
    Nobuta, Kan
    Wu, Xiaohui
    Notibala, Varun
    Demirci, Caghan
    Meyers, Blake C.
    Wang, Guo-Liang
    Ji, Guoli
    Li, Qingshun Q.
    GENOME RESEARCH, 2011, 21 (09) : 1478 - 1486
  • [33] Benchmarking differential abundance analysis methods for correlated microbiome sequencing data
    Yang, Lu
    Chen, Jun
    BRIEFINGS IN BIOINFORMATICS, 2023, 24 (01)
  • [34] TOOLS, METHODS, AND STRATEGIES - THE BENCHMARKING EFFORT FOR NETWORKING CHILDRENS HOSPITALS (BENCHMARK)
    PORTER, JE
    JOINT COMMISSION JOURNAL ON QUALITY IMPROVEMENT, 1995, 21 (08): : 395 - 406
  • [35] Extensive and deep sequencing of the Venter/HuRef genome for developing and benchmarking genome analysis tools
    Zhou, Bo
    Arthur, Joseph G.
    Ho, Steve S.
    Pattni, Reenal
    Huang, Yiling
    Wong, Wing H.
    Urban, Alexander E.
    SCIENTIFIC DATA, 2018, 5
  • [36] Extensive and deep sequencing of the Venter/HuRef genome for developing and benchmarking genome analysis tools
    Bo Zhou
    Joseph G. Arthur
    Steve S. Ho
    Reenal Pattni
    Yiling Huang
    Wing H. Wong
    Alexander E. Urban
    Scientific Data, 5
  • [37] Benchmarking metagenomic binning tools on real datasets across sequencing platforms and binning modes
    Han, Haitao
    Wang, Ziye
    Zhu, Shanfeng
    NATURE COMMUNICATIONS, 2025, 16 (01)
  • [38] TRENDseq-A highly multiplexed high throughput RNA 3′ end sequencing for mapping alternative polyadenylation
    Ogorodnikov, Anton
    Danckwardt, Sven
    MRNA 3' END PROCESSING AND METABOLISM, 2021, 655 : 37 - 72
  • [39] Analysis of Alternative Splicing and Alternative Polyadenylation in Populus alba var. pyramidalis by Single-Molecular Long-Read Sequencing
    Hu, Hongyin
    Yang, Wenlu
    Zheng, Zeyu
    Niu, Zhimin
    Yang, Yongzhi
    Wan, Dongshi
    Liu, Jianquan
    Ma, Tao
    FRONTIERS IN GENETICS, 2020, 11
  • [40] Benchmarking long-read RNA-sequencing analysis tools using in silico mixtures
    Dong, Xueyi
    Du, Mei R. M.
    Gouil, Quentin
    Tian, Luyi
    Jabbari, Jafar S.
    Bowden, Rory
    Baldoni, Pedro L.
    Chen, Yunshun
    Smyth, Gordon K.
    Amarasinghe, Shanika L.
    Law, Charity W.
    Ritchie, Matthew E.
    NATURE METHODS, 2023, 20 (11) : 1810 - 1821