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.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
Updated GEO accessions to reflect changes made by the authors of https://doi.org/10.1101/2022.05.29.493705 (see also https://twitter.com/seankenneths/status/1562119284993695746)
Copyright
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.
Posted August 29, 2022.
