/StrandSeq-NO-pipeline

Primary LanguageRMIT LicenseMIT

StrandSeq-NO-pipeline

Small snakemake pipeline to visualise Nucleosome Occupancy using ngsplot tool.

  1. Create a directory and symlink your samples processed using ashleys-qc-pipeline
mkdir /scratch/TEST & cd /scratch/TEST
ln -s /scratch/DATA/sample_1 .
ln -s /scratch/DATA/sample_2 .
ln -s /scratch/DATA/sample_3 .
  1. Modify configuration

Open config/config.yaml, modify the dir (here /scratch/TEST) and the comparisons list to be processed. Each comparison must correspond to new entry (defined by a -) where all samples are specified without quotes and separated by a , (NO SPACES!)

  1. Run the pipeline
snakemake --profile workflow/snakemake_profiles/HPC/slurm_EMBL