# BAM2GFF

**Repository Path**: clover163/BAM2GFF

## Basic Information

- **Project Name**: BAM2GFF
- **Description**: No description available
- **Primary Language**: Unknown
- **License**: MIT
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2023-12-14
- **Last Updated**: 2024-05-31

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

===== BAM2GFF: Genomic Region READ DENSITY distribution =====

#### === Changelog
1) USAGE

Executable anywhere as long as the PATHTO is correctly specified.
> BAM2GFF-call.sh ["GTF file"] ["BAM file"] ["CHROM SIZES"] ["SAMPLENAME"]


2) DIRECTORY structure

    ├── LICENSE

    ├── README.md

    ├── lib

        └── utils.py   : utilities method
    │   

    └── bin

        ├── BAM2GFF-call.sh    : bash wrapper script
    
        ├── BAM2GFF_main.py    : calculates density of .bam reads in .gff regions
    
        ├── BAM2GFF_gtftogenes.py    : splits .gff into genomic regions (promoter, upstream, downstream, gene region)
    
        └── BAM2GFF_plots.R    : plots matplots and heatmaps of regions provided

    Total: 2 directories, 7 files


3) DEPENDENCIES

	* samtools
	* R version > 3.4
	* python3


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