使用lr-kallisto进行长读测序转录组量化
Rebekah K Loving1, Delaney K Sullivan1,2, A Sina Booeshagi3
1Division of Biology and Biological Engineering, California Institute of Technology, USA.
bioRxiv : the preprint server for biology
|July 29, 2024
概括
准确的全长转录异形量化现在可以通过长读序列数据实现. 新的lr-kallisto工具,通过外体捕获进行了改进,可以快速准确地定量RNA丰度.
科学领域:
- 基因组学和生物信息学
- 分子生物学分子生物学
- 文字转录学 (Transcriptomics) 是一个学科.
背景情况:
- 高通量短读测序使得常规基因水平的RNA丰度定量成为可能.
- 准确和负担得起的全长转录异型的量化仍然是一个重大挑战.
- 转录单体的复杂性和遗传变异使量化工作复杂化.
研究的目的:
- 为了应对使用长读序列数据的最终全长转录异形量化挑战.
- 开发和验证一个计算工具,用于准确的长读RNA量化.
- 评估外体捕获对长读量化准确性的影响.
主要方法:
- lr-kallisto的开发, kallisto的适应用于长时间读取的测序数据.
- 利用牛津纳米孔 (ONT) 测序数据用于方法开发和测试.
- 整合了外汇捕获技术,以评估量化准确度的改进.
主要成果:
- 证明了长时间读取的RNA测序数据的快速和准确量化是可行的.
- 表明外体捕获显著提高了长读数据量化的准确性.
- lr-kallisto成功地将现有的量化方法适用于长期阅读的技术.
结论:
- 长读测序技术与lr-kallisto相结合,可以实现常规的最终同型量化.
- 外体捕获是一个有价值的策略,可以提高长时间读取的转录量化的精度.
- 这项工作克服了长时间读取数据分析的关键生物信息学挑战,以解决转录异形.
相关概念视频
03:21RNA-seq
9.9K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
9.9K
02:24Ribosome Profiling
3.5K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
3.5K