Overview

This repository provides input sample sheets for running data through the scUTRquant pipeline as well as scripts for downloading the raw data. The results of these pipelines were analyzed in the scUTRquant manuscript, which 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

Use

Each folder here can be placed in the input/ directory of the scUTRquant pipeline. That is, when setting up the pipeline, one can do:

## download scUTRquant
git clone https://github.com/Mayrlab/scUTRquant.git

## download inputs
git clone https://github.com/Mayrlab/scUTRquant-inputs.git scUTRquant/input

Each folder contains code to download the raw data. Most of these are in the form of Snakemake pipelines. For example, one can download the Tabula Muris dataset with:

cd scUTRquant/input/tmuris
snakemake --use-conda

Once the data has downloaded, one can run scUTRquant from the root of the scUTRquant/ folder:

snakemake --use-conda --configfile input/tmuris/config_scutr_quant.yaml