===== 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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