Benchmarking UMI-based single-cell RNA-seq preprocessing workflows
Background Single-cell RNA-sequencing (scRNA-seq) technologies and associated
analysis methods have rapidly developed in recent years. This includes preprocessing …
analysis methods have rapidly developed in recent years. This includes preprocessing …
Comparative analysis of common alignment tools for single-cell RNA sequencing
RS Brüning, L Tombor, MH Schulz, S Dimmeler… - …, 2022 - academic.oup.com
Background With the rise of single-cell RNA sequencing new bioinformatic tools have been
developed to handle specific demands, such as quantifying unique molecular identifiers and …
developed to handle specific demands, such as quantifying unique molecular identifiers and …
Accurate quantification of single-cell and single-nucleus RNA-seq transcripts using distinguishing flanking k-mers
In single-cell and single-nucleus RNA sequencing, the coexistence of nascent
(unprocessed) and mature (processed) mRNA poses challenges in accurate read mapping …
(unprocessed) and mature (processed) mRNA poses challenges in accurate read mapping …
Statistical analysis supports pervasive RNA subcellular localization and alternative 3'UTR regulation
Targeted low-throughput studies have previously identified subcellular RNA localization as
necessary for cellular functions including polarization, and translocation. Furthermore, these …
necessary for cellular functions including polarization, and translocation. Furthermore, these …
A like-for-like comparison of lightweight-mapping pipelines for single-cell RNA-seq data pre-processing
Abstract Recently, Booeshaghi and Pachter published a benchmark comparing the kallisto-
bustools pipeline for single-cell data pre-processing to the alevin-fry pipeline. Their …
bustools pipeline for single-cell data pre-processing to the alevin-fry pipeline. Their …