# 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_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 `