AI Article Synopsis
- K-mer indexing is an effective technique for searching RNA sequences in RNA-seq libraries but hasn't allowed for direct quantification of RNA until now.
- The study demonstrates that arbitrary RNA sequences can be quantified quickly and accurately by breaking them down into k-mers, achieving precision similar to traditional methods.
- Using an extensive RNA-seq sample collection from the Cancer Cell Line Encyclopedia, the researchers showcase how k-mer indexing can uncover non-reference sequences and variant RNAs related to specific genetic changes.
Article 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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Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11468207 | PMC |
| http://dx.doi.org/10.1186/s13059-024-03413-5 | DOI Listing |
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