Hi, I am trying to run the ROSE_main.py script. However, we found nearly half of the refseq IDs could not be recognized by ROSE in our study .

The command line is: ROSE_geneMapper.py -g hg38 -i test.txt --list symbol2refseq_G1.txt -o /home/suiyi/YSY/ROSE-1.3.1

It returned that: Traceback (most recent call last): File "/home/suiyi/YSY/ROSE-1.3.1//bin/ROSE_geneMapper.py", line 291, in <module> main() File "/home/suiyi/YSY/ROSE-1.3.1//bin/ROSE_geneMapper.py", line 277, in main enhancerToGeneTable,geneToEnhancerTable =mapEnhancerToGene(annotFile,enhancerFile,uniqueGenes=True,byRefseq=options.refseq, transcribedFile=transcribedFile) File "/home/suiyi/YSY/ROSE-1.3.1//bin/ROSE_geneMapper.py", line 55, in mapEnhancerToGene tssLoci.append(ROSE_ [synbol2refseq_G1.txt](https://github.com/stjude/ROSE/files/8549768/synbol2refseq_G1.txt) utils.makeTSSLocus(geneID,startDict,0,0)) File "/home/suiyi/YSY/ROSE-1.3.1/lib/ROSE_utils.py", line 527, in makeTSSLocus start = startDict[gene]['start'][0] KeyError: 'NM_001002847'

Once the transcript ID 'NM_001002847' was deleted, the run will go on until reporting the next refseq ID it could not recognize. The genelist was transferred by biomaRt in R. The unrecognized ID almost accounted for half of the genelist. Any help is appreciated. Thank you very much！

Best regards, Yan Siyuan 2022/04/25

The python3 version ROSE was downloaded from https://github.com/stjude/ROSE . samtools 1.15.1, bedtools v2.30.0, R version 4.1.3, Python 3.9.12 have been installed.