/ROSE

ROSE: RANK ORDERING OF SUPER-ENHANCERS

Primary LanguagePythonOtherNOASSERTION

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/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