Nucleosome Dynamics Help - Singularity
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_singularityRunning 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 runwill run the container for you.--bind /path/to/data_dir/:/path/to/data_dirwill make thedata_dirwhere input files are stored available to the containernucleosome_dynamics_singularity_latest.sifis 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 pairedRunning 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