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ROSE : RANK ORDERING OF SUPER-ENHANCERS

CLONED using SOURCETREE from: https://bitbucket.org/young_computation/rose/src/master/

Changes from Source.

  1. USAGE

    PATHTO=/path/to/ROSE
    PYTHONPATH=$PATHTO/lib
    export PYTHONPATH
    export PATH=$PATH:$PATHTO/bin
    
    ROSE_main.py [options] -g [GENOME] -i [INPUT_REGION_GFF] -r [RANKBY_BAM_FILE] -o [OUTPUT_FOLDER] [OPTIONAL_FLAGS]
  2. Update:

    • ROSE is executable independent of software directory location.
    • ROSE is compatible with python3
    • ROSE as a docker image: ghcr.io/stjude/abralab/rose:latest
  3. REQUIREMENTS:

    1. All files : All input files much be in one directory.

    2. Annotation file : Annotation file should be in UCSC table track format (https://genome.ucsc.edu/cgi-bin/hgTables). Annotation file should be saved as [GENOME]_refseq.ucsc (example: hg19_refseq.ucsc). Annotation file should be in annotation/ folder in the input files directory.

    3. BAM files (of sequencing reads for factor of interest and control) : Files must have chromosome IDs starting with "chr" Files must be sorted and indexed using SAMtools in order for bamToGFF.py to work. (http://samtools.sourceforge.net/samtools.shtml)

    4. Peak file of constituent enhancers : File must be in GFF format with the following columns:

       column 1: chromosome (chr#)
       column 2: unique ID for each constituent enhancer region
       column 4: start of constituent
       column 5: end of constituent
       column 7: strand (+,-,.)
       column 9: unique ID for each constituent enhancer region
      

      NOTE: if value for column 2 and 9 differ, value in column 2 will be used

  4. DIRECTORY structure

    ├── LICENSE.txt
    │
    ├── README.md
    │
    ├── bin
    │   ├── ROSE_bamToGFF.py : calculates density of .bam reads in .gff regions
    │   ├── ROSE_callSuper.R : ranks regions by their densities, creates cutoff
    │   ├── ROSE_geneMapper.py : assigns stitched enhancers to genes
    │   └── ROSE_main.py : main program
    └── lib
        └── ROSE_utils.py : utilities method
    
    Total: 2 directories, 8 files
    
  5. DEPENDENCIES

    • samtools
    • R version > 3.4
    • bedtools > 2
    • python3