Homotrimer barcodes enable accurate counting of RNA molecules during high-throughput RNA sequencing
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Publisher
Springer Science and Business Media LLC
Link
https://www.nature.com/articles/s41592-024-02169-x.pdf
Reference5 articles.
1. van Dijk, E. L., Jaszczyszyn, Y. & Thermes, C. Library preparation methods for next-generation sequencing: tone down the bias. Exp. Cell Res. 322, 12–20 (2014). This review highlights the sources of bias associated with RNA-seq library preparation.
2. Cha, R. S. & Thilly, W. G. Specificity, efficiency and fidelity of PCR. Genome Res. 3, S18–S29 (1993). This article shows that PCR amplifies different molecules with unequal probabilities.
3. Potapov, V. & Ong, J. L. Examining sources of error in PCR by single-molecule sequencing. PLoS One 12, e0169774 (2017). This paper shows the effect of PCR error rate on the types of mistakes that occur during amplification.
4. Smith, T. S., Heger, A. & Sudbery, I. UMI-tools: modelling sequencing errors in unique molecular identifiers to improve quantification accuracy. Genome Res. 27, 491–499 (2017). This is the gold standard computational method for demultiplexing UMIs in bulk and single-cell RNA sequencing applications.
5. Philpott, M. et al. Nanopore sequencing of single-cell transcriptomes with scCOLOR-seq. Nat. Biotechnol. 39, 1517–1520 (2021). This previous paper from our lab presents scCOLOR-seq long-read sequencing. This method utilizes homodimer nucleotide blocks, integrated into beads, to mitigate sequencing errors.
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