I am currently running RNA-seq analysis on rat mRNA in Galaxy using a flow that uses TopHat2 then cufflinks to determine FPKMs. When I run cufflinks, however, some of the geneIDs get mapped to multiple loci on the genome with varying hits as shown below.
NM_001008876 - - NM_001008876 - - chr10:4284438-4326284 - - 24.3459 20.5645 25.0729 OK
NM_001008876 - - NM_001008876 - - chr13:40006284-40007070 - - 7.2634 4.27328 7.56582 OK
NM_001008876 - - NM_001008876 - - chr17:51085969-51086776 - - 17.9851 11.5232 16.8103 OK
As far as I can tell the gene only exists on chr 10 so I am unsure what it is mapping to. Is this an issue in the file I am inputting or some issue with the parameters? I am aligning to the UCSC, group: Gene and Gene prediction, track: RefSeq Genes, outpuf: GTF.