A Caltech Library Service

Accurate quantification of single-nucleus and single-cell RNA-seq transcripts

Hjorleifsson, Kristján Eldjárn and Sullivan, Delaney K. and Holley, Guillaume and Melsted, Páll and Pachter, Lior (2022) Accurate quantification of single-nucleus and single-cell RNA-seq transcripts. . (Unpublished)

[img] PDF - Submitted Version
Creative Commons Attribution No Derivatives.


Use this Persistent URL to link to this item:


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.

Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription Paper
Hjorleifsson, Kristján Eldjárn0000-0002-7851-1818
Sullivan, Delaney K.0000-0002-8359-6705
Melsted, Páll0000-0002-8418-6724
Pachter, Lior0000-0002-9164-6231
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 All code for simulations and downstream analyses is available at The authors have declared no competing interest.
Record Number:CaltechAUTHORS:20230316-182779000.60
Persistent URL:
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:120170
Deposited By: George Porter
Deposited On:17 Mar 2023 23:02
Last Modified:17 Mar 2023 23:02

Repository Staff Only: item control page