===== ROSE: RANK ORDERING OF SUPER-ENHANCERS =====
LICENSE: Information in LICENSE.txt.
CLONED using SOURCETREE from: https://bitbucket.org/young_computation/rose/src/master/
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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]
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Update:
- ROSE is executable independent of software directory location.
- ROSE is compatible with python3
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REQUIREMENTS:
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All files : All input files much be in one directory.
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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.
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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)
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Peak file of constituent enhancers : File must be in GFF format with the following columns: 1: chromosome (chr#) 2: unique ID for each constituent enhancer region 4: start of constituent 5: end of constituent 7: strand (+,-,.) 9: unique ID for each constituent enhancer region NOTE: if value for column 2 and 9 differ, value in column 2 will be used
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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 -
DEPENDENCIES
- samtools
- R version > 3.4
- bedtools > 2
- python3
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