Published June 8, 2022
| Supplemental Material + Submitted
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Pseudoalignment facilitates assignment of error-prone Ultima Genomics reads
- Creators
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Booeshaghi, A. Sina
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Pachter, Lior
Abstract
We analyze single-cell RNA-seq data sequenced with Ultima Genomics technology and find high error rates in and near homopolymers. To compensate for these errors, we explore the use of pseudoalignment for read assignment, and find that it can perform better than standard read alignment. Our pseudoalignment read assignment for Ultima Genomics data is available as part of the kallisto-bustools kb-python package available at https://github.com/pachterlab/kb_python.
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. Version 1 June 5, 2022; Version 2 - June 14, 2022. Methods: The code to reproduce all the figures and results in the preprint is available at https://github.com/pachterlab/BP_2022 and provides a complete description of the methods. Data Availability: All data used in this preprint is available on GEO under accession GSM5917802.Attached Files
Submitted - 2022.06.04.494845v2.full.pdf
Supplemental Material - media-1.pdf
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Additional details
- Eprint ID
- 115049
- Resolver ID
- CaltechAUTHORS:20220607-425123000
- Created
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2022-06-08Created from EPrint's datestamp field
- Updated
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2022-06-30Created from EPrint's last_modified field
- Caltech groups
- Division of Biology and Biological Engineering