Question: Multiple mapping to one gene ID using Cufflinks in Galaxy
gravatar for mgtrax10
3.5 years ago by
United States
mgtrax100 wrote:

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.

Thank you,


cufflinks galaxy • 824 views
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