slam-k562-utrome

This repository provides a pipeline for reprocessing the SLAM-seq dataset from Wu et al., 2019 at 3'UTR isoform resolution using the human UTRome annotation.

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

Reproducing the Pipeline

Cloning

This repository can be cloned with:

git clone https://github.com/Mayrlab/slam-k562-utrome.git

Prerequisite Software

This requires Conda/Mamba and Snakemake. If you do not already have a Conda installation, we strongly recommend Miniforge. We provide a YAML for the Snakemake version we used (v6.8), but feel free to use later versions.

Configuration

Three configuration options in config.yaml should be adjusted by the user prior to running:

• tmp_dir: temporary directory for scratch
• genome_fa: FASTA file of hg38 genome
• utrome_gtf: GTF file of human UTRome (obtainable through scUTRquant)

Running

The full pipeline can be executed with simply

snakemake --use-conda

We encourage HPC users to configure a Snakemake profile and use this via a --profile argument.