snm3C-seq

This is a workflow for process snm3C-seq data using Yet Another Pipeline and other associated packages.

Table of Contents

• snm3C-seq
  • Table of Contents
  • Usage

Usage

1. Clone this repo. You can run git clone https://github.com/vari-bbc/snm3C-seq.git <path/to/new_folder>. The cloned folder will be your working directory.

2. Move your sequencing reads to raw_data/.

3. Modify the config files and samplesheet:

• config/config.yaml - This file defines the locations of required configuration files.
• <yap_config> - The path to this file is defined in config/config.yaml. This is the config file for YAP. Note that this workflow has only been tested with the hisat3n aligner option.
• config/samplesheet/units.tsv
  • fq1 - name of read1 fastq
  • fq2 - name of read2 fastq
• config/allcools_regions_and_quantifiers.tsv defines settings for allcools generate-dataset --regions and --quantifiers. See allcools documentation.
  • region_name - name of the region set
  • regions - either an integer setting bin size or an absolute path to a regions file.
  • quantifiers - space-delimited string setting the quantification type, nucelotide context and cutoff. See documentation for --quantifiers parameter.

4. If your lab has their own nodes on the VAI HPC, add the partition name to line 4 in the SLURM profile (profile/generic_slurm/config.v9+.yaml). For example, you may modifify it to -p yourlab,long,short \.

5. Start the workflow by running sbatch bin/run_snake.slurm. Monitor the jobs from this workflow by running squeue -u user.name.

6. Check the snake_workflow.e log file to see if the workflow ran to completion. Run tail snake_workflow.e; there should be a line that says 100% completed or something to that effect.