pegRNA Linker Identification Tool (pegLIT), a powerful tool developed by David Liu lab, can automatically identify non-interfering nucleotide linkers between a pegRNA and 3' motif.
Here I wrote some custom scripts to run peglit using multithreads.
Download this repository.
wget https://github.com/Shall-We-Dance/peglit/archive/refs/heads/main.zip
unzip main.zip
Install environment using conda, which is much easier than compiling from source code.
conda env create -f peglit.yaml
Activate the conda environment.
conda activate peglit
Open run_peglit.py and specify THREAD_NUM, INPUT_FILE, OUTPUT_FILE and MOTIF, then just run the script.
python run_peglit.py
We also provided an example input pegRNA_input_example.csv in this repository, and the output of it should be the same as pegRNA_result_example.csv.