Baiting out a full length sequence from unmapped RNA-seq data.
Baiting out a full length sequence from unmapped RNA-seq data.
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DOI：
10.1186/s12864-021-08146-4
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发表时间：
2021-11-27
期刊：
影响因子：
4.4
通讯作者：
Zhang Y
中科院分区：
文献类型：
--
作者：
Li D;Huang Q;Huang L;Wen J;Luo J;Li Q;Peng Y;Zhang Y
作为一种强有力的工具，RNA-Seq已被广泛应用于各种研究中。通常，未映射的RNA-seq读取被认为是无用的，被丢弃或忽略。我们开发了一种策略，通过未映射阅读结合特定的反转录引物设计和高通量测序来挖掘全长序列。在本研究中，我们从标准的RNASeq数据中回收了36个未映射的阅读片段，并随机选择了一个149个 碱基片段作为模型。设计了特定的逆转录引物来扩增其两端，然后进行下一代测序。然后，我们设计了一个基于幂分布的统计模型来估计它的完整性和重要性。此外，我们通过Sanger测序对其进行了验证。结果表明，该基因全长1556 ，微卫星结构存在插入突变。我们相信这种方法将是从未映射的RNA-seq数据中提取序列信息的有用策略。此外，这也是获得未知基因全长序列的另一种方法。网上版载有补充材料，可在10.1186/s12864-021-08146-4查阅。
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. 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. 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. The online version contains supplementary material available at 10.1186/s12864-021-08146-4.
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影响因子：
46.9
作者：
Trapnell C;Williams BA;Pertea G;Mortazavi A;Kwan G;van Baren MJ;Salzberg SL;Wold BJ;Pachter L
通讯作者：
Pachter L
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
3
作者：
Sangiovanni, Mara;Granata, Ilaria;Guarracino, Mario Rosario
通讯作者：
Guarracino, Mario Rosario
DOI：
10.1073/pnas.85.23.8998
发表时间：
1988-12-01
影响因子：
11.1
作者：
FROHMAN, MA;DUSH, MK;MARTIN, GR
通讯作者：
MARTIN, GR
影响因子：
4.4
作者：
McIntyre LM;Lopiano KK;Morse AM;Amin V;Oberg AL;Young LJ;Nuzhdin SV
通讯作者：
Nuzhdin SV