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