Transipedia.org: k-mer-based exploration of large RNA sequencing datasets and application to cancer data

IF 10.1 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genome Biology Pub Date : 2024-10-10 DOI:10.1186/s13059-024-03413-5

Chloé Bessière, Haoliang Xue, Benoit Guibert, Anthony Boureux, Florence Rufflé, Julien Viot, Rayan Chikhi, Mikaël Salson, Camille Marchet, Thérèse Commes, Daniel Gautheret

引用次数: 0

Abstract

Indexing techniques relying on k-mers have proven effective in searching for RNA sequences across thousands of RNA-seq libraries, but without enabling direct RNA quantification. We show here that arbitrary RNA sequences can be quantified in seconds through their decomposition into k-mers, with a precision akin to that of conventional RNA quantification methods. Using an index of the Cancer Cell Line Encyclopedia (CCLE) collection consisting of 1019 RNA-seq samples, we show that k-mer indexing offers a powerful means to reveal non-reference sequences, and variant RNAs induced by specific gene alterations, for instance in splicing factors.

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Transipedia.org：基于 k-mer 的大型 RNA 测序数据集探索及其在癌症数据中的应用

事实证明，依靠k-mers的索引技术能在成千上万的RNA-seq文库中有效地搜索RNA序列，但却无法实现直接的RNA定量。我们在此证明，通过将任意RNA序列分解成k-mers，可以在几秒钟内对其进行量化，其精确度与传统的RNA量化方法类似。利用由 1019 个 RNA-seq 样本组成的癌症细胞系百科全书（CCLE）的索引，我们展示了 k-mer 索引为揭示非参考序列和由特定基因改变（如剪接因子）诱导的变异 RNA 提供了一种强有力的手段。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

21.00

自引率

3.30%

发文量

241

审稿时长

2 months

期刊介绍： Genome Biology stands as a premier platform for exceptional research across all domains of biology and biomedicine, explored through a genomic and post-genomic lens. With an impressive impact factor of 12.3 (2022),* the journal secures its position as the 3rd-ranked research journal in the Genetics and Heredity category and the 2nd-ranked research journal in the Biotechnology and Applied Microbiology category by Thomson Reuters. Notably, Genome Biology holds the distinction of being the highest-ranked open-access journal in this category. Our dedicated team of highly trained in-house Editors collaborates closely with our esteemed Editorial Board of international experts, ensuring the journal remains on the forefront of scientific advances and community standards. Regular engagement with researchers at conferences and institute visits underscores our commitment to staying abreast of the latest developments in the field.