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


依赖于 k-mer 的标定技术已被证明可以有效地在数千个 RNA-seq 文库中搜索 RNA 序列，但不能直接进行 RNA 定量。我们在这里表明，任意 RNA 序列可以通过分解成 k-mer 在几秒钟内进行定量，其精度类似于传统的 RNA 定量方法。使用由 1019 个 RNA-seq 样本组成的癌细胞系百科全书 （CCLE） 集合的索引，我们表明 k-mer 索引提供了一种强大的方法来揭示非参考序列和由特定基因改变诱导的变体 RNA，例如剪接因子。