CUT&Tag workflow

Usage

NOTE This workflow is optimized for the HPC @ Van Andel Institute.

Step 1: Configure the workflow

• Move your fastq sequences to raw_data/
• Look over the config file under bin/, make sure the references are correct. Do not change modules.
• Set up the sample sheet (samples.tsv). You may find it helpful to run ./make_samples_template.sh from inside the bin/ subdirectory to get a template file based on the files in raw_data/. The columns are:
  • sample - Name of the sample. Fastqs will be renamed to this.
  • control - You can use 'NA'. Leaving it blank should also be fine.
  • fq1 - Name of read1 fastq
  • fq2 - Name of read2 fastq
  • sample_group - You can use the same information as sample column.
• If you used make_samples_template.sh, you need to rename the generated template file to "samples.tsv".

Step 2: Run the workflow

• From the root directory of the project (where Snakefile is located), run sbatch bin/run_snakemake.sh.