Baiting out a full length sequence from unmapped RNA-seq data

Abstract Background As a powerful tool, RNA-Seq has been widely used in various studies. Usually, unmapped RNA-seq reads have been considered as useless and been trashed or ignored. Results We develop a strategy to mining the full length sequence by unmapped reads combining with specific reverse tra...

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Autores principales:	Dongwei Li, Qitong Huang, Lei Huang, Jikai Wen, Jing Luo, Qing Li, Yanling Peng, Yubo Zhang
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Unmapped reads Full length sequence Statistical model RNA-seq Biotechnology TP248.13-248.65 Genetics QH426-470
Acceso en línea:	https://doaj.org/article/64905360506f4e71be749e7023442c74
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spelling	oai:doaj.org-article:64905360506f4e71be749e7023442c742021-11-28T12:23:16ZBaiting out a full length sequence from unmapped RNA-seq data10.1186/s12864-021-08146-41471-2164https://doaj.org/article/64905360506f4e71be749e7023442c742021-11-01T00:00:00Zhttps://doi.org/10.1186/s12864-021-08146-4https://doaj.org/toc/1471-2164Abstract Background As a powerful tool, RNA-Seq has been widely used in various studies. Usually, unmapped RNA-seq reads have been considered as useless and been trashed or ignored. Results We develop a strategy to mining the full length sequence by unmapped reads combining with specific reverse transcription primers design and high throughput sequencing. In this study, we salvage 36 unmapped reads from standard RNA-Seq data and randomly select one 149 bp read as a model. Specific reverse transcription primers are designed to amplify its both ends, followed by next generation sequencing. Then we design a statistical model based on power law distribution to estimate its integrality and significance. Further, we validate it by Sanger sequencing. The result shows that the full length is 1556 bp, with insertion mutations in microsatellite structure. Conclusion We believe this method would be a useful strategy to extract the sequences information from the unmapped RNA-seq data. Further, it is an alternative way to get the full length sequence of unknown cDNA.Dongwei LiQitong HuangLei HuangJikai WenJing LuoQing LiYanling PengYubo ZhangBMCarticleUnmapped readsFull length sequenceStatistical modelRNA-seqBiotechnologyTP248.13-248.65GeneticsQH426-470ENBMC Genomics, Vol 22, Iss 1, Pp 1-8 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Unmapped reads Full length sequence Statistical model RNA-seq Biotechnology TP248.13-248.65 Genetics QH426-470
spellingShingle	Unmapped reads Full length sequence Statistical model RNA-seq Biotechnology TP248.13-248.65 Genetics QH426-470 Dongwei Li Qitong Huang Lei Huang Jikai Wen Jing Luo Qing Li Yanling Peng Yubo Zhang Baiting out a full length sequence from unmapped RNA-seq data
description	Abstract Background As a powerful tool, RNA-Seq has been widely used in various studies. Usually, unmapped RNA-seq reads have been considered as useless and been trashed or ignored. Results We develop a strategy to mining the full length sequence by unmapped reads combining with specific reverse transcription primers design and high throughput sequencing. In this study, we salvage 36 unmapped reads from standard RNA-Seq data and randomly select one 149 bp read as a model. Specific reverse transcription primers are designed to amplify its both ends, followed by next generation sequencing. Then we design a statistical model based on power law distribution to estimate its integrality and significance. Further, we validate it by Sanger sequencing. The result shows that the full length is 1556 bp, with insertion mutations in microsatellite structure. Conclusion We believe this method would be a useful strategy to extract the sequences information from the unmapped RNA-seq data. Further, it is an alternative way to get the full length sequence of unknown cDNA.
format	article
author	Dongwei Li Qitong Huang Lei Huang Jikai Wen Jing Luo Qing Li Yanling Peng Yubo Zhang
author_facet	Dongwei Li Qitong Huang Lei Huang Jikai Wen Jing Luo Qing Li Yanling Peng Yubo Zhang
author_sort	Dongwei Li
title	Baiting out a full length sequence from unmapped RNA-seq data
title_short	Baiting out a full length sequence from unmapped RNA-seq data
title_full	Baiting out a full length sequence from unmapped RNA-seq data
title_fullStr	Baiting out a full length sequence from unmapped RNA-seq data
title_full_unstemmed	Baiting out a full length sequence from unmapped RNA-seq data
title_sort	baiting out a full length sequence from unmapped rna-seq data
publisher	BMC
publishDate	2021
url	https://doaj.org/article/64905360506f4e71be749e7023442c74
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Baiting out a full length sequence from unmapped RNA-seq data

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