use ROSE to identify super enhancer

Question

[CL]

hey everyone, i want to use ROSE to identify super enhancer and to see if there is difference in the super enhancer after some treatment in lung cancer cell line i see that this is the typical use:

[user@cn3107 ~]$ ROSE_main.py -h 
Usage: ROSE_main.py [options] -g [GENOME] -i [INPUT_REGION_GFF] -r [RANKBY_BAM_FILE] -o [OUTPUT_FOLDER] [OPTIONAL_FLAGS]

Options:
  -h, --help            show this help message and exit
  -i INPUT, --i=INPUT   Enter a .gff or .bed file of binding sites used to
                        make enhancers
  -r RANKBY, --rankby=RANKBY
                        bamfile to rank enhancer by
  -o OUT, --out=OUT     Enter an output folder
  -g GENOME, --genome=GENOME
                        Enter the genome build (MM9,MM8,HG18,HG19,MM10,HG38)
  -b BAMS, --bams=BAMS  Enter a comma separated list of additional bam files
                        to map to
  -c CONTROL, --control=CONTROL
                        bamfile to rank enhancer by
  -s STITCH, --stitch=STITCH
                        Enter a max linking distance for stitching
  -t TSS, --tss=TSS     Enter a distance from TSS to exclude. 0 = no TSS
                        exclusion

i do have the bam files but i didn't understand how to get the enhancer file in gf/bed format and also how to install this program on my computer. i would like to get any explanation

[Matthias Zepper]

You first need to provide coordinates of enhancers specific to your cell type yourself. There are ample of databases to download reference coordinates from and several methods to call them yourself given various types of available input data (ChIP-seq, ATAC-seq, CAGE-seq etc.). See section 1.3 of my thesis supplement for a brief overview as of 2019.

For running ROSE, I think, it is the easiest to use the Docker container.