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CDseq

setting up the workflow

  1. Add your raw .fastq files to raw_data/
  2. Update bin/samples.tsv to reflect the samples in your dataset.
  3. Make sure the information in bin/config.yaml is correct, in particular the genome index, anntaiton file, and genome sequences.
  4. After samples.tsv and config.yaml files are fully setup, load the snakemake module as "module load bbc/snakemake/snakemake-5.28.0". Then, do a dry-run using "snakemake -np". If everything works, the screen will show a list of jobs that the pipeline will run.
  5. When ready to run the pipeline, do "qsub ./bin/run_snake.sh". This will start the job.