CoSTseq (Co-transcriptional structure tracking)

Data processing pipeline and analysis code for handling CoSTseq and DMS-MaPseq sequencing data sets.

Installing the CoSTseq package

CoSTseq uses Snakemake and a custom conda environment. In addition, the following software packages need to be installed and accessible for Snakemake: fastp, STAR, UMICollapse, RNAstructure, samtools. Set the path to each software package in the config/snake_CoST.yaml file.

# clone repository
git clone https://github.com/NeugebauerLab/CoSTseq.git
cd CoSTseq

# create conda environment
conda env create --name CoST --file=CoST_env.yml # create new environment from template
conda activate CoST # activate

# install python package
pip install -e .

Running the data processing pipeline

After completing the configuration process, the pipeline can be executed using the following command:

conda activate CoST
snakemake -c 16 -d smk_rundir/test --configfile config/snake_CoST.yaml --resources mem_mb=32000 --rerun-incomplete --use-conda

Re-generating analyses and figures from "Rapid folding of nascent RNA regulates eukaryotic RNA biogenesis"

To re-generate the analyses, first run the analysis pipeline on deposited raw data, or download processed files from GEO accession number GSE254264. Save the processed data files in the data directory. Analysis code for each individual figure is available in jupyter notebooks in the notebooks directory and can be executed directly.