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

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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Publication Details

Journal
Genome biology
Published
2024-10-10
DOI
https://doi.org/10.1186/s13059-024-03413-5
Citations
7
Primary Topic
RNA modifications and cancer
Type
article
Field-Weighted Citation Impact
1.64

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article

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

Haoliang Xue, Thérèse Commes, Florence Rufflé, Daniel Gautheret et al.
7 citations
Genome biology
RNA modifications and cancer
1.64
article

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

Haoliang Xue, Thérèse Commes, Florence Rufflé, Daniel Gautheret, Camille Marchet, Benoît Guibert, Rayan Chikhi, Julien Viot, Chloé Bessière, Anthony Boureux, Mikaël Salson
article en
7 citations

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.

Genome biologyVol. 25(1)
Centre National de la Recherche Scientifique (FR), Université Toulouse III - Paul Sabatier (FR), Inserm (FR), Institut Pasteur (FR), Université Paris Cité (FR), Université de Lille (FR), Commissariat à l'Énergie Atomique et aux Énergies Alternatives (FR), Université Paris-Saclay (FR), Centre de Recherches en Cancérologie de Toulouse (FR), Methodology and Quality of Life Unit in Oncology (FR), Institute for Regenerative Medicine & Biotherapy (FR), CEA Paris-Saclay (FR), Hôpital Saint Eloi (FR), École Centrale de Lille (FR), Université de Franche-Comté (FR)
Agence Nationale de la Recherche
Openalex Percentile: Top 16%
RNA modifications and cancer
1.64
DOIOpen Access PDFOpenAlex
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