A snakemake pipline for demuxing quantseq pools. Mainly a re-implementation of the protocol in the quantseq pool github, and uses their demux program
To demux quantseq pool data, use the 'bulk_to_bam' folder. You must change the filepaths in the config.yaml to match your system, and run "snakemake --n-cores {n cores}" You also must download the quantseq demux program: https://github.com/Lexogen-Tools/idemux as well as STAR, cutadapt, SAMTOOLS, and umi-tools