Bioinformatics for Novel Long Intergenic Noncoding RNA (lincRNA) Identification in Skeletal Muscle Cells

  • Xianlu Peng
  • Kun Sun
  • Jiajian Zhou
  • Hao Sun
  • Huating WangEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1556)


Long intergenic noncoding RNAs (lincRNAs) have emerged as critical participators in gene regulation in myriads of cell types. The development of the whole transcriptome sequencing technology, or RNA-seq, has enabled novel lincRNA detection, but the bioinformatics analysis toward distinguishing reliable ones remains a challenge. Here, we describe the bioinformatics workflow developed for identifying novel lincRNAs step by step, including read alignment, transcriptome assembly and transcript filtering.

Key words

lincRNA RNA-seq Bioinformatics Skeletal muscle cells 



The work is substantially supported by seven General Research Funds (GRF) to H.W. and H.S. from the Research Grants Council (RGC) of the Hong Kong Special Administrative Region, China (Project Code: 14133016, 14100415, 14102315, 14116014, 14113514, 476113 and 473713).


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Copyright information

© Springer Science+Business Media LLC 2017

Open Access This chapter is distributed under the terms of the Creative Commons Attribution Noncommercial License, which permits any noncommercial use, distribution, and reproduction in any medium, provided the original author(s) and source are credited.

Authors and Affiliations

  • Xianlu Peng
    • 1
    • 2
  • Kun Sun
    • 1
    • 2
  • Jiajian Zhou
    • 1
    • 2
  • Hao Sun
    • 1
    • 2
  • Huating Wang
    • 3
    • 4
    Email author
  1. 1.Department of Chemical PathologyThe Chinese University of Hong KongHong KongChina
  2. 2.Li Ka Shing Institute of Health SciencesThe Chinese University of Hong KongHong KongChina
  3. 3.Department of Orthopaedics and TraumotologyThe Chinese University of Hong KongHong KongChina
  4. 4.507A, Li Ka Shing Institute of Health SciencesPrince of Wales Hospital, The Chinese University of Hong KongHong KongChina

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