Peaks Workflow

This workflow is designed to align, perform basic QC and call peaks for peak-based methods such as ChIP-seq, CUT&RUN and ATAC-seq.

Usage

1. git clone <repo> <new_directory_name>

2. Put the 'fastq.gz' files in the raw_data/ subdirectory. You may use symlinks.

3. Look over the config file to ensure that the correct indexes and other species-specific settings are used.

4. 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:

   i.sample -- Name of the sample. Fastqs will be renamed to this. You may use the same 'sample' name in multiple rows in this file to represent fastqs that should be cat together.

   ii. control -- 'sample' name for the control to be used, for example, as control for MACS2. If not applicable, use 'NA'. Leaving it blank should also be fine.

   iii. fq1 -- R1 file

   iv. fq2 -- R2 file; fill in with NA if SE data.

   v. sample_group -- Grouping variable for replicates.

   vi. enriched_factor -- Samples with the same enriched_factor will be normalized together with CSAW, if alternative normalization is requested in the config file.

5. From the root directory of the project, run sbatch bin/run_snakemake.sh.