Published December 3, 2022
| Submitted
Discussion Paper
Open
Accurate quantification of single-nucleus and single-cell RNA-seq transcripts
Chicago
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Abstract
The presence of both nascent and mature mRNA molecules in single-cell RNA-seq data leads to ambiguity in the notion of a "count matrix". Underlying this ambiguity, is the challenging problem of separately quantifying nascent and mature mRNAs. We address this problem by relating k-mer assignment to read assignment in the context of different classes of molecules, and describe a unified approach to quantifying both single-cell and single-nucleus RNA-seq.
Additional Information
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license. Code availability. kallisto is available under the BSD-2-Clause license. The version used for this paper is available at https://github.com/pachterlab/kallisto-D. All code for simulations and downstream analyses is available at https://github.com/pachterlab/HSHMP_2022. The authors have declared no competing interest.Attached Files
Submitted - 2022.12.02.518832v1.full.pdf
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2022.12.02.518832v1.full.pdf
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Additional details
- Eprint ID
- 120170
- Resolver ID
- CaltechAUTHORS:20230316-182779000.60
- Created
-
2023-03-17Created from EPrint's datestamp field
- Updated
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2023-03-17Created from EPrint's last_modified field
- Caltech groups
- Division of Biology and Biological Engineering (BBE)