Published October 10, 2022
| Version Supplemental Material + Submitted
Discussion Paper
Open
Quantifying orthogonal barcodes for sequence census assays
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1.
California Institute of Technology
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2.
Massachusetts Institute of Technology
Abstract
Barcode-based sequence census assays utilize custom or random oligonucloetide sequences to label various biological features, such as cell-surface proteins or CRISPR perturbations. These assays all rely on barcode quantification, a task that is complicated by barcode design and technical noise. We introduce a modular approach to quantifying barcodes that achieves speed and memory improvements over existing tools. We also introduce a set of quality control metrics, and accompanying tool, for validating barcode designs.
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 4.0 International license. The authors have declared no competing interest.Attached Files
Submitted - 2022.10.09.511501v1.full.pdf
Supplemental Material - media-1.pdf
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2022.10.09.511501v1.full.pdf
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Additional details
Identifiers
- Eprint ID
- 120314
- Resolver ID
- CaltechAUTHORS:20230322-101653000.21
Related works
- Describes
- https://github.com/pachterlab/BMGP_2020 (URL)
- https://github.com/pachterlab/kb_python/ (URL)
- https://github.com/pachterlab/qcbc/ (URL)
Dates
- Created
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2023-03-22Created from EPrint's datestamp field
- Updated
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2023-03-22Created from EPrint's last_modified field