/BAM2GFF

BAMtoGFF, matrix density, plot visualizations

Primary LanguagePythonOtherNOASSERTION

===== 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"]

  1. 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

  2. DEPENDENCIES

    • samtools
    • R version > 3.4
    • python3

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