Hi all, I'm getting some odd micro RNA FPKM values in my cufflinks output that I'm trying to troubleshoot. The MIRs will show a large FPKM value in one sample, but a zero FPKM in the other samples which seems incorrect. I did some by eye checks in IGV and can't see why this would be.
Here's an example of what I mean.
The data in IGV doesn't seem to agree with the FPKM values either. Here's MIR3125 viewed in IGV as an Example.
Am I maybe missing a cufflinks or tophat option that would avoid this?
Thanks for any help.
Here's an example of what I mean.
The data in IGV doesn't seem to agree with the FPKM values either. Here's MIR3125 viewed in IGV as an Example.
Am I maybe missing a cufflinks or tophat option that would avoid this?
Thanks for any help.
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