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 Fansler et al., bioRxiv, 2023.
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