How "upSearch" "downsearch" "upstream" "downstream" in "ROSE_utils.py" were defined?

[Jun]

Hi Brian, Sorry to bother. Strictly speaking, this is even not an "issue". I was just browsing the script, in "ROSE_utils.py" when defining "makeTranscriptCollection", "makeTSSLocus", arguments like ""upSearch" "downsearch" "upstream" "downstream" were specified. I could tell they should be integers specifying the genomic ranges, but have no ideas how they were defined or determined. Or maybe they were specified in some way, I just missed it. Could you please kindly advise me about that? Thanks! Jun

[Jun]

in ROSE_main (line 101): ROSE_utils.makeTSSLocus(geneID,startDict,50,50) and ROSE_geneMapper(line 49): ROSE_utils.makeTranscriptCollection(annotFile,0,0,500,transcribedGenes) they are specified. Sorry...