RPA-wrapper

Ribose Preferred Analysis Wrapper Scripts

Table of Contents

1. Installation
• Getting the code
• Creating the enviroment with required dependencies
• Additional Dependencies
2. Usage
• Defining variables
• Initializing functions and activating enrviroment
• Running the Code
• Statistical test for preference and genotype comparisons
• Generating Stacked barplots for hotspots
3. Contributing
4. License
5. Contact
6. Citations

Installation

Getting the code

The development version from GitHub with: sh git clone https://github.com/xph9876/RibosePreferenceAnalysis.git git clone https://github.com/DKundnani/RPA-wrapper.git

Creating the enviroment with required dependencies

sh conda env create --name RPAwrapper_env --file /RPA-wrapper/env.yml

Additional Dependencies

• Input files (bed) containing single nucleotide locations, mainly for rNMP data. (another single nucleotide data can also be experimented on!)
• Reference genome files (.fa and .fai) of the organism being used(Also used to generate bed files)
• ranges/bed file fo the genome locations to be analyzed and for which background frequency will be calculated as well.
• order file, example in repository

Usage

Defining variables

```bash scripts='path/to/RibosePreferenceAnalysis/' #location of RPA repository ref='path/to/reference/sacCer2/sacCer2.fa' #Reference Fast file range='path/to/ranges/sacCer2/nucl.bed' #Example ranges of nuclear genome of sacCer2

range='path/to/chrM.bed'

bed='path/to/bed/' #Folder of bed files order='path/to/order' #sample file share in the RPA-wrapper repository ```

Initializing functions and activating enrviroment

bash conda activate RPAwrapper_env #activating enviroment source path/to/RPA-wrapper/Heatmapwrapper.sh

Running the Code for both strands

```bash mkdir heatmaps; cd heatmaps #make the output directory and run the code from it

Generating Background frequency of the genome

bgfreq $scripts $ref $range #one time for each range samplefreq $scripts $ref $range $bed #Generating frequency of libraries/samples normfreq $scripts $ref $range $bed #Normalizing sample frequency to genome frequency resortplot $scripts $ref $range $bed $order #resort the matrices as per order file and hence the heatmaps rm sample_freq/$(basename $range .bed)/*bed #Cleanup ```

Running the Code for single strand - gives out same and opposite for the range with 6th column having strand information

```bash mkdir heatmaps; cd heatmaps #make the output directory and run the code from it

Generating Background frequency of the genome

bgfreqss $scripts $ref $range ; bgfreqos $scripts $ref $range samplefreqss $scripts $ref $range $bed ; samplefreqos $scripts $ref $range $bed normfreqss $scripts $ref $range $bed ; normfreqos $scripts $ref $range $bed resortplotss $scripts $ref $range $bed $order ; resortplotos $scripts $ref $range $bed $order rm sample_freq/$(basename $range .bed)/*bed #Cleanup ```

Statistical test for preference and genotype comparisons

bash mww $scripts $ref $range $bed $order

Generating Stacked barplots for hotspots

bash Rscript path/to/RPA-wrapper/comp.R -m sorted_chrM_mono_0 #hotspot composition files usually contain on entry for every genotype.

Contributing

Contributions are what make the open source community such an amazing place to learn, inspire, and create. Any contributions you make are greatly appreciated.

If you have a suggestion that would make this better, please fork the repo and create a pull request. You can also simply open an issue with the tag "enhancement". Don't forget to give the project a star! Thanks again!

1. Fork the Project
2. Create your Feature Branch (git checkout -b feature/AmazingFeature)
3. Commit your Changes (git commit -m 'Add some AmazingFeature')
4. Push to the Branch (git push origin feature/AmazingFeature)
5. Open a Pull Request

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License

Distributed under the GNU GPL3 License. See LICENSE.txt for more information.

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Contact

Deepali L. Kundnani - deepali.kundnani@gmail.com

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Citations

Use this space to list resources you find helpful and would like to give credit to. I've included a few of my favorites to kick things off!+ * Distinct features of ribonucleotides within genomic DNA in Aicardi-Goutières syndrome (AGS)-ortholog mutants of Saccharomyces cerevisiae Deepali L. Kundnani, Taehwan Yang, Alli L. Gombolay, Kuntal Mukherjee, Gary Newnam, Chance Meers, Zeel H. Mehta, Celine Mouawad, Francesca Storici bioRxiv 2023.10.02.560505; doi:https://doi.org/10.1101/2023.10.02.560505 * Kundnani, D. (2024). rNMP_hotspots:2.0.0 (2.0.0). Zenodo. https://doi.org/10.5281/zenodo.8152090

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