Analyzing Locksmith-designed probe capture methylation sequencing results
Clone the repository with the following command:
$ git clone https://github.com/RoySimons96/Lockpick.git
Enter the repository by cd Lockpick.
- Download Conda with Python 3.9
wget https://repo.anaconda.com/archive/Anaconda3-2021.11-Linux-x86_64.sh
Install Conda
bash Anaconda3-2021.11-Linux-x86_64.sh
- Snakemake (at least v4.3.1) and biopython-1.79
Install Mamba into your Conda-based python distribution
conda install -n base -c conda-forge mamba
Activate the Conda base environment (which now includes Mamba).
conda activate base
Create a new conda environment called Lockpick with snakemake in it.
mamba create -c conda-forge -c bioconda -n snakemake Lockpick
Activate the Lockpick conda environment.
conda activate Lockpick
Check whether Snakemake is successfully installed by running the following command:
snakemake --help
Install the following packages: biopython=1.79 .
conda install python=3.9
conda install -c conda-forge biopython=1.79
conda install -c bioconda cutadapt=4.5
conda install -c bioconda multiqc=1.18
conda install -c bioconda fastqc=0.12.1
Go into the Lockpick directory by:
cd <Path to Lockpick>
Make sure to activate the conda environment by:
conda activate Lockpick
snakemake --cores [amount of cores] --configfile [path to config file]
The configuration file which is needed to run Lockpick includes all initial parameters needed to analyze sequencing data created by capture using a Locksmith probe panel.
"path_to_config_file": The path in which the configuration file can be found.
"path_to_work_dir": The path where temporary files are created.
"path_to_scripts": The directory in which the Lockmith python scripts are situated.
"output_directory": The path of the directory in which the output files will be created.
"chosen_panel_csv": The Locksmith designed probe panel file, used for recognizing probe arms and to construct the amplicon reference file.
"reference_genome_path": The path to the FASTA format of the human reference genome to be used.
"fastq_folder": The path to the folder in which the to be analyzed FASTQ files are located.
"target_cpg_bed": The path to the bedfile which states the targets used for probe design.
"bismark_flags": Flags used when running bismark.
"cutadapt_flags": Flags used when running cutadapt for adapter removal.
"samples": a list of sample names to be used for analysis.
Note that the expected format for the fastq files is {sample}_{read}.fq, where {sample} is taken from the "samples" input and {read} either denotes a 1 or a 2, for the forward and reverse read respectively.