ROSE usage for mm39 genome

[Brahmandam-Gayatri]

Hello,

Thank you for ROSE for calling super-enhancers. I have a query: How can I make the refseq table for mm39 and use it for stitching the super-enhancers of my ChIP-seq data?

In addition, I am getting the following error:

MAKING TSS COLLECTION
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Traceback (most recent call last):
  File "/path/to/file/ROSE/bin/ROSE_geneMapper.py", line 299, in <module>
    main()
  File "path/to/file/ROSE/bin/ROSE_geneMapper.py", line 282, in main
    enhancerToGeneTable,geneToEnhancerTable,withGenesTable = mapEnhancerToGene(annotFile,enhancerFile, uniqueGenes=True, byRefseq=options.refseq, subtractInput=options.control, transcribedFile=transcribedFile)
                                                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/path/to/file/ROSE/bin/ROSE_geneMapper.py", line 140, in mapEnhancerToGene
    closestGene = allEnhancerGenes[distList.index(min(distList))]
                  ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
IndexError: list index out of range

Command used:

ROSE_main.py -g MM39 -i /path/to/file/treated1.bed -r /path/to/file/treated1.sorted.bam -c /path/to/file/treated1_input.sorted.bam -o . -s 12500 -t 2500

I have tried to make a refseq file for mm39 genome as specified in the instructions. Hence any help in this regard is highly appreciated.

Thanks & regards,
Gayatri.