Abstract
RNA-sequencing could be nowadays considered the gold standard to study the coding and noncoding transcriptome. The great advantage of high-throughput sequencing in the characterization and quantification of long noncoding RNA (lncRNA) resides in its capability to capture the complexity of lncRNA transcripts configuration patterns, even in the presence of several alternative isoforms, with superior accuracy and discovery power compared to other technologies such as microarrays or PCR-based methods. In this chapter, we provide a protocol for lncRNA analysis using through high-throughput sequencing, indicating the main difficulties in the annotation pipeline and showing how an accurate evaluation of the procedure can help to minimize biased observations.
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Acknowledgments
SB is supported by the Italian Ministry of Education, University and Research (PRIN 2017 #2017PPS2X4_003), and the Italian Association of Cancer Research, AIRC, Milan, Italy (Investigator Grant IG2017 #20052). LA is supported by the Accelerator Award #29374 through CRUK-AIRC partnership.
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Agnelli, L., Bortoluzzi, S., Pruneri, G. (2021). Bioinformatic Pipelines to Analyze lncRNAs RNAseq Data. In: Navarro, A. (eds) Long Non-Coding RNAs in Cancer. Methods in Molecular Biology, vol 2348. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1581-2_4
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DOI: https://doi.org/10.1007/978-1-0716-1581-2_4
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