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

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.

SUBMITTER: Bessiere C 

PROVIDER: S-EPMC11468207 | biostudies-literature | 2024 Oct

REPOSITORIES: biostudies-literature