Nucleosome Dynamics - Singularity

Nucleosome Dynamics Singularity image is a containerized implementation of 'Nucleosome Dynamics suite'.

Nucleosome Dynamics

Nucleosome Dynamics is a suite of R programs for nucleosome-related analyses based on MNase-seq experimental data. The toolkit includes the following analyses:

• nucleR: define and classify the location of nucleosomes from MNase-seq data.
• Nucleosome Dynamics: compares different MNase-seq experiments identifying variations in nucleosomes location.
• NFR: locate nucleosome-free regions
• Periodicity: predicts nucleosome phasing at gene level
• TSS: classify transcription start sites based on the surrounding nucleosomes
• Stiffness: computes nucleosome stiffness derived from a Gaussian function fitting

Container software

This singularity image extends and distributes the following rellevant software:

• R libraries:
  • NucleR R library: https://github.com/nucleosome-dynamics/nucleR
  • Nucleosome Dynamics R library: https://github.com/nucleosome-dynamics/NucDyn
• R programs:
  • Nucleosome Dynamics analyses: https://github.com/nucleosome-dynamics/nucleosome_dynamics

Running Nucleosome Dynamics

Before using Singularity, you've to install singularity, if not previously done, you can do it by following the instructions from [Singularity install] (https://singularity.lbl.gov/docs-installation#install-the-master-branch)

The Singularity image for Nucleosome Dynamics can be found at singularity hub as nucleosome-dynamics/nucleosome_dynamics_singularity. The image can be pulled by following the next command.

singularity pull shub://nucleosome-dynamics/nucleosome_dynamics_singularity

Running an individual analysis

You can run manually your containers using the following command:

singularity run --bind /path/to/data_dir/:/path/to/data_dir nucleosome_dynamics_singularity_latest.sif   [analysis] [analysis_options]

A short description of the parameters would be:

• singularity run will run the container for you.
• --bind /path/to/data_dir/:/path/to/data_dir will make the data_dir where input files are stored available to the container
• nucleosome_dynamics_singularity_latest.sif is the image name, which can be found at [singularity hub] (https://singularity-hub.org/collections/2579).
• [analysis] [analysis_options] correspond to the analysis type you want to run and its paremeters.

Available analysis are:

[analysis]	Description
readBAM	Read Aligned MSase-seq BAM into a RData structure (required for further process)
nucleR	Determine the positions of the nucleosomes across the genome
NFR	Short regions depleted of nucleosomes
txstart	Classify Transciption start accordint to the properties of surrounding nucleosomes
periodicity	Periodic properties of nucleosomes inside gene bodies
stiffness	Aparent stiffness constant foreach nucleosome obtained by fitting the coverage to a gaussian distribution
nucleR_stats	Nucleosome call statistics
nucDyn	Comparison of two diferent MNase-seq experiments to nucleosome architecture local changes
NFR_stats	Nucleosome Free Regions statistics
txstart_stats	TSS and TTS statistics
periodicity_stats	Statistics on Nucleosome periodicity
stiffness_stats	Statistics on stiffness
nucDyn_stats	Statistics on Nucleosome Dynamics analysis

Each analysis has its own input files and arguments. singularity run nucleosome_dynamics_singularity_latest.sif [analysis] --help will display such information in detail. Yet, a full usage description can be found at the Nucleosome Dynamics repository.

Example

Here is an example on how to load a MNase-seq reads file using readBAM. It takes as input a BAM file and convert it into an RData file ready to be feed to other analyses ('nucleR', 'NFR', etc.)

singularity run --bind $PWD/test/data/:$PWD/test/data nucleosome_dynamics_singularity_latest.sif readBAM --input $PWD/test/data/cellcycleG2_chrII.bam --output $PWD/test/data/cellcycleG2_chrII.RData --type paired

Running a workflow script

You can combine different analysis tools to build your own workflow, you can do it following this command:

singularity run --bind /path/to/data_dir/:/path/to/data_dir nucleosome_dynamics_singularity_latest.sif  run  [WF_file_path]

Where:

• WF_file_path: is a bash file containing the Rscript calls to different analyses.

Example

Here is an example on how to run the test workflow file test/scripts/wf-test.sh, a bash file sequencially calling all 'Nucleosome Dynamics' analyses.

singularity run --bind $PWD/test/data:$PWD/test/data nucleosome_dynamics_singularity_latest.sif  run $PWD/test/scripts/wf-test.sh