Transipedia.org: k-mer-based exploration of large RNA sequencing datasets and application to cancer data.
Bioinformatics
Non-coding RNA
RNA-processing
RNA-seq
Transcriptomics
Journal
Genome biology
ISSN: 1474-760X
Titre abrégé: Genome Biol
Pays: England
ID NLM: 100960660
Informations de publication
Date de publication:
10 Oct 2024
10 Oct 2024
Historique:
received:
26
03
2024
accepted:
01
10
2024
medline:
11
10
2024
pubmed:
11
10
2024
entrez:
10
10
2024
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 39390592
doi: 10.1186/s13059-024-03413-5
pii: 10.1186/s13059-024-03413-5
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
266Subventions
Organisme : Agence Nationale de la Recherche
ID : ANR-22- CE45-0007
Organisme : Agence Nationale de la Recherche
ID : ANR-19-CE45-0008
Organisme : Agence Nationale de la Recherche
ID : ANR-19-P3IA-0001
Informations de copyright
© 2024. The Author(s).
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