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.