I am using tophat2/cufflinks/cuffmerge to precess my data. When I checked the results from cufflinks, I found all novel transcripts' exons locate on same chromosomes. It looks really strage to me. Should there be some novel transcripts with interchromesomal exons? My code is like this :

tophat2 -p 8 -G /path/to/hg38_tran/hg38_ucsc.annotated.gtf -o /path/to/output/dir/$name hg38 $pair1 $pair2
cufflinks -p 8 -g /path/to/hg38_tran/hg38_ucsc.annotated.gtf -o path/to/output/dir/$name /path/to/tophat2/results/$dir

I have got advice about using histat/stringtie instead of tophat/cufflinks. But the software I used for downstream analysis only support result from cufflinks. So I am kind of stuck here.

Any advice is appreciated.

Thank you.