problem when running ROSE

[Former user]

Hi:

I met the following problem when I tried to use ROSE, could you help me check it. All the python, R, samtools works fine with my system (centOS).

USING H3K27ac.gff AS THE INPUT GFF USING mm9_refseq.ucsc AS THE GENOME Traceback (most recent call last): File "/n/home06/fgu/pu_lab/tools/young_computation-rose-abb68ec8668f/ROSE_main.py", line 471, in <module> main() File "/n/home06/fgu/pu_lab/tools/young_computation-rose-abb68ec8668f/ROSE_main.py", line 322, in main annotFile = genomeDict[genome] KeyError: 'mm9_refseq.ucsc'

Fei

[young_computation]

Hi Fei,

sorry for the late response. It looks like your -g flag argument is wrong. Please flag the genome build (i.e. -g mm9) as opposed to the actual file. The ROSE program will find the correct annotation file if it is in the appropriate folder structure.

Please see the example data here for more guidance http://younglab.wi.mit.edu/super_enhancer_code.html

data and examples are here: http://younglab.wi.mit.edu/ROSE/ROSE_DATA.zip