Overview

This repository provides analysis of peak widths of 10X Chromium 3' end data across 28 libraries from Tabula Muris at a set of cleavage sites curated for minimal internal priming upstream of the cleavage site.

The accompanying manuscript is openly available at:

Fansler, M.M., Mitschka, S. & Mayr, C. Quantifying 3′UTR length from scRNA-seq data reveals changes independent of gene expression. Nat Commun 15, 4050 (2024). https://doi.org/10.1038/s41467-024-48254-9

Organization

The input count data is provide in two forms:

• raw: muris.coverage.partial.tsv.gz
• clean: tmuris.coverage.partial.clean800.tsv.gz

The analysis reported in Fansler et al., bioRxiv, 2023 is found in the empirical_quantiles.ipynb IPython notebook.

Additional notebooks are included as alternative model-based approaches, but were not used in the publication.

Software enviroment

The environment.yaml file provides a record of software versions used to run the notebooks. This was originally executed on macOS and is only expected to be recreatable on macOS systems.