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Pipeline based on snakemake to process ChIP-seq (with optional spike-in based normalisation), ATAC-seq, RNA-seq and short read WGS data for SNP calling. The defaults are optimised for the Milne group directory on the CCB cluster, but can be easily modified for other groups and clusters.

Quick Start¶

Installation¶

The installation page has detailed instructions for installing SeqNado. For a very quick start, run the following command:

mamba install -c bioconda seqnado

Set up the pipeline¶

Config file¶

Generate the config file and a working directory for the pipeline:

seqnado-config [atac|chip|rna|snp]

Ensure files are in the correct location¶

Ensure that the fastq files, and design are in the correct location:

# Fastq files
ln -s /path/to/fastq_files/* /path/to/working-directory/made-by-seqnado-config/fastq/

Design (optional)¶

The design will be generated automatically if not provided and the samples follow the correct naming convention.

cd /path/to/working-directory/made-by-seqnado-config/
seqnado-design [atac|chip|rna|snp]

Run the pipeline¶

cd /path/to/working-directory/made-by-seqnado-config/
seqnado [atac|chip|rna|snp] -c <number of cores> --preset [ss|ls] 
# ss = use cluster, ls = use local (not recommended)
# additional options
--queue/-q [short|long] --scale-resource/-s <factor to multiply resources> 

# An actual example would be:
seqnado rna -c 8 --preset ss