small-RNA-bioinformatics-code

This project provides a collection of scripts for analyzing small RNA sequencing data. The main functionality is centered around generating nucleotide density plots, visualizing read distributions, and processing sequencing data files.

Project Structure

• src/: Contains the source code for the project.

  • nucleotide_density_plot.py: Generate density plots from BAM files
  • barcode_splitter.py: Split FASTQ files by barcode sequences
  • SAM_read_counter.py: Count and extract reads from SAM files
  • utils/: Utility functions package

• tests/: Unit tests and test data

• data/: Example datasets and file formats

• docs/: Documentation and usage examples

• requirements.txt: Python package dependencies

Installation

# Clone the repository
git clone https://github.com/username/small-RNA-bioinformatics-code.git
cd small-RNA-bioinformatics-code

# Install dependencies
pip install -r requirements.txt

Usage

Nucleotide Density Plots

python src/nucleotide_density_plot.py --input <input.bam> \
                                     --output <output.pdf> \
                                     --chromosome chr1 \
                                     --start 1000 \
                                     --end 2000 \
                                     --rpm 1.5 \
                                     --norm-factor 0.5

Barcode Splitting

python src/barcode_splitter.py --input <input.fastq> \
                              --output-dir output/ \
                              --barcodes AGCG:PP333 CGTC:PP334

SAM Read Counting

python src/SAM_read_counter.py --input <input.sam> \
                              --output filtered.sam \
                              --chromosome chr1 \
                              --start 1000 \
                              --end 2000 \
                              --max-length 30

Command Line Arguments

Common Arguments

• --input: Input file path (BAM/SAM/FASTQ)
• --output: Output file path
• --output-dir: Output directory for split files

Nucleotide Density Plot

• --chromosome: Target chromosome name
• --start: Region start position
• --end: Region end position
• --rpm: Reads per million
• --norm-factor: Normalization factor

Barcode Splitter

• --barcodes: Space-separated list of "sequence:name" pairs
• Allows 1 mismatch in barcode matching
• Removes barcode from sequence after matching

SAM Read Counter

• --chromosome: Target chromosome
• --start: Region start position
• --end: Region end position
• --max-length: Maximum read length (default: 30)

Citation

If you use this code in your research, please cite:

Spracklin G, Fields B, Wan G, Becker D, Wallig A, Shukla A, Kennedy S. The RNAi Inheritance Machinery of Caenorhabditis elegans. Genetics. 2017 Jul;206(3):1403-1416. doi: 10.1534/genetics.116.198812. PMID: 28533440; PMCID: PMC5500139.

Contributing

Contributions are welcome! Please submit a pull request or open an issue for any suggestions or improvements.